Follow Anderson and the on-screen tutorial messages. Eventually you come to a wall with Husks climbing up it. Don't bother trying to shoot them all, as they are infinite in number. As Anderson says he's run out of ammo, follow him down the ladder to the right and shoot Husks until you yourself run out of ammo. Melee the last few Husks to death, then go in the room nearby. Loot the Med-Kit on the floor for some XP (looting Medi-Gel from Kits or Stations always gives XP, even if your Medi-Gel is not full). A cutscene follows with some more opportunities for morality points. After another cutscene, walk over the Thermal Clips to pick them up, then reload your weapon.
Continue on. After your conversation with the soldiers, some Cannibals will attack. Kill them, then Talk to the soldiers again. Cross the bridge and loot the Med-Kit to the left. Kill some more Cannibals, moving forward when you can. On your way to the Radio, pick up the M-8 Avenger assault rifle, then Use the Radio. More Cannibals will attack from the way you came. Either kill them all or run out of ammo. Whichever occurs first, the Normandy SR-2 will then arrive to save you. After a series of cutscenes, you wind up on the surface of Mars. After your first dialog choice, there's a Paragon Interrupt Opportunity.
A long conversation ensues, during which you'll have some morality point choices. At the end of the scene, Liara replaces James in your squad, so allocate Talent Points for her. Finish off the guards on the upper level here. If you don't have biotics yourself, use Liara's, as the game suggests. Once the area is clear, your goal is to get up to the balcony level. First, loot the Med-Kit to the right. You'll then need to find and Use the Vehicle Lift to open your path. Then climb up the crates to the left and jump onto the now-raised vehicle, then across to the balcony. Go through the door.
You'll need to kill a bunch of Cerberus Troops in the first room. In the second room, Read a DataPad for some XP (Reading DataPads always grants XP). In the next room is another DataPad on a bench. In a weapons Locker is the Ariake Technologies Gauntlets. (Sadly, you cannot change armor until you're back on the Normandy.) Continue on a bit to pick up the M-4 Shuriken SMG, and then a Med-Kit. In the next room, Use the Security Console to trigger some dialog, then go through the now-unlocked door.
Go down the ladder and around the corner. Note the view. Continue on and pick up the Kassa Fabrication Chestplate. Go up the ladder and back inside. Go around and down the first flight of stairs. Search the tables to the right to find a DataPad. Continue down the next flight of stairs and you'll see and hear some Cerberus troops. They can't hear or see you, so take cover and shoot them through the glass. When they're dead, hop over the wall to where they were, pick up the SMG Scope upgrade and loot the Med-Station. Use the Environmental Controls to trigger another conversation.
Go through the nearby door. Pick up the SMG Ultralight Materials upgrade and Read the DataPad before going up the stairs. Use the nearby Weapons Bench to alter your loadout and apply the upgrades you've picked up so far. Go through the next door to kill some more Cerberus troops. In the first hallway is a DataPad. Around the corner to the left is another hallway with more Cerberus troops. When they're clear, Activate either of the Clean Room Sterilization Controls when the beams are at their widest point, so that the door to the right inside the room is approachable. Inside, you'll find a Sniper Rifle Extended Barrel upgrade, a Shotgun High Caliber Barrel upgrade, a Med-Kit, and a DataPad.
Go through the next door, and to the right you'll find the M-23 Katana shotgun. Through the next door you'll be shot at by a ceiling-mounted turret. Follow the tutorial to learn how to move from cover to cover until you make it all the way around the room and Liara says it's clear. (Note that the Infiltrator's Tactical Cloak doesn't work against this turret.)
Open the next door and kill the Cerberus troops inside. When they're dead, find a Med-Kit on the right, and DataPad and a Sniper Rifle Concentration upgrade further in the room. Use the Auto-Turret Controls to trigger a dialog and cutscene. When it's done, you'll get a brief explanation on how to order your squad. Follow its surprisingly useful suggestions and kill the Cerberus troops who get off the Tram. Get on the tram yourself, which gets stuck halfway there. Kill the troops on the car that comes alongside, then jump over to and use that car to get to the end.
When the windows open, you'll be in another fight. After clearing the area, pick up the Shotgun Shredder upgrade to the right, loot the Med-Station in the center, and find the M-15 Vindicator assault rifle ahead to the left. (I recommend choosing the Change Loadout option when you do, in order to pick a pistol with a faster fire rate, if you have one. This is to make the end of the Mission easier.) When you're ready, go through the next door.
You'll find yourself in a large circular room. Ashley/Kaidan goes off to search the area, while Shepard and Liara have a conversation with the Illusive Man. At the end of the dialog, Dr. Eva will start running away, and there will be a range display in the lower right of the screen. If she gets more than 40m away, you fail and have to start the chase all over again. If you get too close, she'll hit you with Incinerate, which causes you to stumble for a couple of meters. There's no point in attacking her, as she'll just instantly recharge her shields. She'll occasionally move barriers in your path, but you can just hop/slide over them.
Eventually, a Cerberus shuttle lands to pick up Dr. Eva. James uses your Kodiak to ram the Cerberus shuttle and knocks it down. Dr. Eva picks up Ashley/Kaidan and slams her/him into the shuttle, causing unconsciousness and serious injury. She then runs towards you in slow motion. You slowly raise your pistol, and your goal is to shoot Dr. Eva until she "dies". (This is why you wanted to swap to a faster pistol earlier.) If she gets to you, it's game over and you have to try again. Remember that headshots do more damage. When she does finally go down, you'll watch several cutscenes, the last of which leaves you on the Citadel.
Avina is nearby and can fill you in on some of the local stuff. Next to the Elevator is Citadel Rapid Transit, which will only take you back to the Normandy, if you're too lazy to just walk around the corner. Get on the Elevator and Use it. For now, there are only two other places to go. First, regardless of what you said earlier, go to Huerta Memorial Hospital.
Behind the front desk are two Asari having a counseling session. Every time you visit the hospital, you can stand nearby and overhear a portion of the commando's story, and her struggles with PTSD. (I absolutely recommend it. Later, on the Spectre Terminal, you'll have the option of granting her a gun. Doing so causes her to ... no longer be here).
Across from the front desk is the Sirta Foundation Store Console. Use it to add it to the list of stores you can access from the Normandy. You'll also want to buy the Medi-Gel Capacity Upgrade, as well as a gift for your injured squadmate.
Behind the Store is Avina, who can tell you about the area.
Near a window you'll find Dr. Chakwas speaking with Dr. Michel. Talk to either of them, and Dr. Michel will walk away, leaving you in dialog with Dr. Chakwas. You can either recruit her to rejoin the Normandy, or tell her to stay in her research post on the Citadel. Not recruiting her makes her a War Asset and makes recruiting Dr. Michel possible. When that conversation is done, Talk to Dr. Michel. If Dr. Chakwas is staying on the Citadel, you can get Dr. Michel to join the Normandy. You can also ask her how your injured squadmate is doing.
Go through the two airlock doors and in the first door on the right in the hall ahead. You'll see Ashley/Kaidan laying on a bed, unconscious and bruised. Choose your morality option. If you want to begin or continue a romance, choose the top option.
Go back to the elevator and go to the Embassies. Talk to Avina to learn about the area. Go left and towards the back to find a volus talking to a seated human. Overhear the conversation to get the Mission Shrike Abyssal: Prothean Obelisk.
To the right of Avina, you'll see a desk with a bunch of people standing around it. Stand near the older human female to hear her sad war story. Like the Asari in the Hospital, this woman's story will advance every time you visit the Embassies.
Up the stairs, the first door on the left is Commander Bailey's Office. Entering puts you in conversation with him. After the initial dialog, re-enter conversation to learn more about him.
Across the hall is Udina's Office. Open the door to start a series of conversations. If your Spectre status was not restored in ME2, it will be restored now, regardless of whether you want it or not. When you regain control of Shepard, you may speak with Udina again, if you like.
Across from Udina's Office is the Spectre Office. Inside and to the right is a weapons range, where you can test the weapons you've gotten so far on some targets. This is useful to avoid starting a mission only to discover you hate the weapons you've got. To the left are the Spectre Requisitions Store, which you'll want to use to get access to it from the Normandy, and the Spectre Console, on which you can read about new Intel, enable Missions, or authorize certain things (like giving a gun to an Asari with PTSD). Check back later in the game for more stuff.
Go back out to Avina, and Talk to Khalisah al-Jilani. If you're nice to her, you can gain her as a War Asset. Otherwise, use the Renegade Interrupts to knock her out. If you don't take that, you'll then get a Paragon Interrupt Opportunity to comfort her.
After you've spoken to the Council, James will be nearby and available to Talk. When you're done, use the Elevator to get back to the Docking Area, and go back to the Normandy.
In the middle of the War Room is the War Terminal. Use it to read about the Assets you pick up during the game. The Galactic Readiness Rating is a percentage based on your use of multiplayer. To get it to 100%, you'll need to play multiplayer. Note that the rating decreases gradually over time if you don't play for awhile, so if you're going to play multiplayer, I recommend waiting until near the end of the single-player game. That being said, if you complete all of the DLC, you'll have more than enough points here to get the "best" ending without needing to play multiplayer. (The minimum Effective Military Strength required for the "best" ending is 3100. Without playing multiplayer to get the Galactic Readiness Rating % up, you can get over 4000 (8000 total) if you collect all the miscellaneous Assets and play all the DLC.)
In the Conference room to the right on the crates is the Model Alliance Shuttle. Through the next door is a security checkpoint, guarded by Privates Campbell and Westmoreland. They occasionally make comments as you pass through. You'll have plenty of time to listen to them, as it takes as long to go through the scan here as it does in the real-life TSA checkpoint.
In the forward most part of Deck 2 you'll find Joker, who will have fun dialog after every Mission. Remember to save before every conversation, as they can't be repeated. If you accidentally skip some dialog or choose the wrong morality option, you'll want to try again. While some characters move around the ship from time to time. He never gets out of this chair.
Next to the Galaxy Map is Specialist Samantha Traynor. Talk to her to get the Mission N7: Cerberus Lab, to learn more about her, and to possibly flirt with her a bit more. She'll never move from this spot.
Also on the aft side of the Galaxy Map is Shepard's Private Terminal (there's also one in the Captain's Cabin). Use it to watch three videos about combat for an Accomplishment, and to read your emails. There will be a flashing green light on it if there are any unread messages. If you have the From Ashes DLC, there will be one that will give you the Mission Priority: Eden Prime (From Ashes DLC)
Use the Elevator to get to the other decks. On Deck 3, go in Life Support to find a Model Destiny Ascension. There are two restrooms here, one for men and one for women. You can only go in the one for Shepard's sex. The other isn't even openable.
If you recruited either Dr. Chakwas or Dr. Michel, she'll be in Med Bay. She'll usually be here, but will be in the Crew Quarters temporarily later in the game. Talk to her to learn what she thinks of being here. Also in Med Bay are two surgical tools: one will allow you to change your Bonus Power, and the other will reset Shepard's and your squadmate's Talent Points. In the AI core is the robotic corpse of Dr. Eva, for now.
Walking around the perimeter of the cafeteria will be Ensign Copeland. He'll either be here or patrolling the Galaxy Map on Deck 2. Later, you may even find him in the Port Observation Lounge on Deck 3. If you stand in front of him he'll stop. You can then force him to salute you.
In Miranda's former office is Liara. The dialog will be different here depending on whether or not you completed the Shadow Broker DLC in ME2. Glyph the VI will give you a tour. Use the Intel Terminal when you've found some Intel from Scanning planets to choose between bonuses. Use the Broker Terminal to read Intel that the Shadow Broker has learned. This will vary depending on your choices throughout the game and what DLC you completed in ME2. Like your Private Terminal, this will have a flashing green light when it has an unread message on it. Liara will either be in here or in Javik's room after you recruit him.
Down to Deck 4. As you get off the elevator, go right, and if you recruited her, Diana Allers will be in Zaeed's former digs. Talk to her and you'll have a morality choice of what you want her to focus on.
Inside Engineering, you'll find Engineer Adams. He'll usually be here, but you may find him later in the Crew Quarters on Deck 3. Talk to him to learn why he's here and to either accept his apology or admonish him for not joining you against the Collectors.
Below Engineering you can find several Models: Shadow Broker Ship, Sovereign, and Turian Cruiser. If you imported an ME2 savegame where you had acquired the Space Hamster, it'll be running around the floor here, and you can catch it.
Deck 5 is the Shuttle Bay. Talk to Steve Cortez, your shuttle pilot and acquisitions officer. If Shepard is Male, you can start a romance with him by flirting with him. He'll always be standing somewhere in the vicinity of the shuttle. Not talking to him at every opportunity results in him dying towards the end of the game.
James Vega is doing pull-ups on the opposite side in the middle of some crates. Talk to him to start a sparring match. There will be several Renegade and Paragon Interrupt opportunities during the fight, though they're easy to miss if you're trying to pay attention to his back story.
If you have the Collector's Edition of the game, wandering around the deck will be a robotic dog. If you stand in front of it, it'll stop and you can say something to it. Stand there long enough, and it'll fall asleep.
There are four desks here. The Armor Locker (also in Captain's Cabin) can be used to change Shepard's casual outfit and combat armor. The Procurement Interface has the same stuff as the stores on the Citadel, though at a 10% markup. New stores will become available after you access them on the Citadel, and they'll carry the exact same stuff. The Weapon Upgrades console allows you to improve your weapons' stats. (It takes about 6 million credits to upgrade all the weapons in the game, so I advise just concentrating on the ones you use.) The Weapon Bench allows you to alter Shepard's loadout, as well as change the upgrade modules on Shepard's weapons. Your squadmates' weapons can only be changed when you start a Mission.
Also on this deck in the crates are several Models: Alliance Fighter, Normandy SR-1, Quarian Liveship, Alliance Cruiser, and Geth Cruiser.
Deck 1 is the Captain's Cabin. Here are duplicates of the Armor Locker and the Private Terminal. On this Private Terminal, unlike the one in the CIC, you can look at your available squad mates and change their combat appearances. When you do, you'll also change the bonus they get from their armor, so click the Info button to see the new bonus.
When a character wants to meet you in your cabin, using the Personal Terminal will start a cutscene with them. Nearby you can see all the Models you've picked up. The Space Hamster will be on a nearby shelf, if you have it. Any fish you've acquired will be in the tanks. You'll want to feed them between Missions, unless you've purchased the Aquarium VI. You can go in the restroom and Use the Toilet, but all it does is flush. (I like to use it as a reminder that I myself need to get up from my computer.) Next to the bed you can toggle the Sound System to listen to music while you're in this cabin.
When you're ready, go to Deck 2 and Access the Galaxy Map to begin exploring.
The following places are available to Explore. You'll want to go to these places to find Intel for the Intel Terminal, as well as find some hidden War Assets.
Sigurd's Cradle: Decoris and Skepsis Systems
Hades Gamma: Antaeus, Cacus, Dis, Farinata, and Plutus Systems
Kite's Nest: Harsa and Untrel Systems
Exodus Cluster: Asgard and Utopia Systems
On the left is a Med-Kit. In the center is a DataPad, and nearby is the M-97 Viper sniper rifle. In the structure to the right of those is another DataPad. Back on the left side you can find the M-27 Scimitar shotgun and an Assault Rifle Piercing Mod. Keep going to find a structure containing the Hahne-Kedar Greaves, a DataPad, and a Med-Kit. Turn around and head back towards the Nav Point. In a structure on the left is a Pistol Piercing Mod, the Armax Arsenal Shoulder Guard, and a Weapon Bench, where you can alter your loadout with all the new weapons and mods you just found. Finally, in the alcove between you and General Corinthus is a DataPad and a Pistol Magazine Upgrade Mod.
Now you can Talk to General Corinthus, who tasks you with repairing the Comm Tower. From the structure you're in, go right, then left and out the gate. When you get to the Tower, choose one squadmate to climb up and repair it, then fend off several Husks. When they're eliminated, return to the General. If Garrus survived ME2, he'll join you here and displace Liara in your squad.
Your next task is to defend the Air Base from Reaper troops. Allocate Garrus's Talent Points. As you make your way out there, be sure to pick up the Assault Rifle Magazine Upgrade Mod, and Salvage some Supplies for Credits on some crates to the right. Fend off the waves of Husks and Marauders, then the General orders you to fend off more enemies at the main gate, so follow the Nav Point and go up the ladder.
Man the Turret and use it to destroy several waves of Husks. Eventually, you'll be knocked off on the wrong side of the barricade, and you'll be attacked by a Brute, accompanied by several more Husks. When the area is clear, proceed along the path until you get the prompt to look at the view. Here you'll find a DataPad. Continue along the path, killing Husks as you go, until you come to some soldiers, where you'll find another DataPad, a Med-Kit, and a Sniper Rifle Spare Ammo Mod.
Continue along the path, and a fighter will crash in front of you. To get past it, go down the path to the left. Further ahead, you'll find a Med-Kit. A little further along you'll witness an explosion, followed by a group of enemies. Once they're clear, go a little further until you're attacked again. On the right just past the first bunker, you'll find a Reaper Blackstar heavy weapon. It works wonders on the Brutes. Just beware that it'll kill your squadmates if they get too close to the blast. There's no need to save it, as this is the last fight.
After the fight, search the area for two Med-Kits and a Sniper Rifle Enhanced Scope Mod. Go up the ramp to trigger a conversation with General Victus. A cutscene puts you back on the Normandy, having a conversation with the Asari Councilor.
If Garrus survived ME2, he'll be available as a squadmate in future Missions, and on the Normandy will usually be in his favorite spot: the Forward Battery on Deck 3, calibrating the weapons.
Talk to everyone on the Normandy, as many of them will have new things to say.
You will meet Mordin Solus if he survived ME2, otherwise, Padok Wiks will accompany you. After the conversation, in the back of the room near the emergency exit on the upper level is an Assault Rifle Extended Barrel Mod. There are two Research Logs you can Use, one in the near the middle of the room on the upper level and another in the lower level down the stairs from the elevator. When you're finally ready to advance, Use the elevator as instructed. When that doesn't work, turn around and use the ladder in the emergency exit to continue.
Open the door and head around the corner where you will see many STG members shooting. Move forward and a Cerberus shuttle arrives to drop off two waves of Assault Troopers. Finish those off and pick up the Shotgun Blade Attachment Mod on the inner wall. You can also Use the Research Log along the right wall to learn why the Yahg are there. Right next to it is a Medical Station. On the bench in the outer corner you will find a DataPad with Credits. Approach the door at the end of the long room and open it. Hop over the wall to your left, then jump across the pit and pick up the Shotgun Spare Ammo Mod. Then jump back across the wall and head up the stairs.
Now you need to move quickly because you need to protect the shield on the pod. If you move quickly you can keep the pod at full integrity. Once you finish off the Cerberus goons, head down the room. On the wall across from the pod is a DataPad worth Credits. Keep moving forward and a cut-scene plays. Don't wait too long to Activate the Quarantine Checkpoint 1, as more Cerberus will show up if you delay.
After the next cutscene, two Assault Troopers attack you from inside a shuttle. Take them out, then go straight ahead through the opening they created in the wall. Around the left corner, a couple of Salarians are trying to hold off a Centurion in the distance. Another shuttle arrives to drop off more Assault Troopers. Take them out, then pick up the Pistol High Caliber Barrel Mod along the left wall on the shelf. Open the door at the end of the room, and proceed around to the left and up the stairs.
If Major Kirahe is present, you will see him kill some Assault Troopers. If Kirahe is not present, Lieutenant Tolan will be there instead, and will get taken out quite quickly, making the battle harder. Kill all the enemies. On the right just inside the room are some Spare Parts that you can Salvage for Credits. At the end of the room on the right, Activate the Species Observation Area in order to advance. Do not move away from the scanner or you will have to wait for activation again.
Just inside the door, there is a Medical Station. Go down the hall and open the door. The area will have another group of Cerberus to fight. In the middle of the room on the lower level are the Armax Arsenal Greaves. Around the corner past the ladder on the lower level is a Sentry Interface and some Spare Parts to Salvage. When you've collected everything, Bypass the door on the upper level to continue.
Take out the enemies in the next room. Hug the right wall from where you came in, and around the corner on a couch is the M-13 Raptor Assault Rifle. Following the left wall from where you came in, you will come to a Pistol Scope Mod next to a Research Terminal. Continue following the left wall around the corner to a Medical Station. In the corner of the same room, the Scorpion heavy pistol will be on the floor in the far right opposite the power terminal. Finally go ahead and Reactivate the Power Terminal, but be prepared to race back to protect the pod, as more bad guys are about to attack. Activate the Quarantine Checkpoint 2 and fight off another wave of Cerberus enemies. The door near where you entered this room is now active. Return there and pass through the door. Jump across the open pit and climb up the ladder.
Sprint into the room because a bunch of Cerberus troops will immediately start attacking the pod if you don't keep them held up. Once you've finished them off, don't delay in releasing the female because if you do, more troops will show up. Once you activate the release, a cutscene will play where an Atlas jumps in. Kill it and the rest of the troops that show up. When the area is clear, you'll get some more cutscenes.
Back on the Normandy, explore the ship and speak to people. The Urdnot leader (either Wrex or Wreav) can now be found in the Normandy's war room, and is available to talk. Primarch Victus will ask to speak with you and offer the mission Tuchanka: Turian Platoon. The female krogan will be named "Eve" and occupy the med-bay with the Salarian scientist. Your doctor, if you have one, will vacate the med bay for the salarian and krogan, and will hang out in the Crew Area with Engineer Adams. This means if you haven't completed it already, you will be unable to progress the Engineer's side mission for Thermal Pipe until after the med bay returns to normal. Allers, if she's on your ship, will be having an argument in her quarters with Ensign Copeland. Choose one to support.
On the Citadel, you can do the following:
Go to Krogan DMZ and Enter Orbit at Tuchanka. Land at the Shroud Facility. The Salarian Dalatrass contacts you with a choice of sabotaging the cure. Regardless of what you say now, the actual choice comes later. During the next conversation, you can choose whether or not to reveal the Dalatrass' offer. Even if you do choose to reveal it, you'll be interrupted before you can say anything.
When you reach the Hollows, you need to fight off waves of Husks swarming the area. In the next cutscene, while traveling, you're given the option again to reveal the Dalatrass' deal or keep quiet about it. The only way for Mordin/Wiks to live is if you don't (see below). Soon after, the convoy comes to an abrupt stop. Running around is recommended, as the area is a treasure trove of loot. You can pick up a Shotgun Smart Choke Mod, a Pistol Magazine Upgrade Mod, a Pistol Melee Stunner Mod, the Death Mask Helmet, the Graal Spike Thrower shotgun and 2 Med-Kits. You can Talk to a Krogan fixing and complaining about a Tomkah's combustion manifold (sound familiar?), and another who was the owner of the Graal you took and wants whatever you kill with it as his "trophies". To kick off the next part of the plot, Talk to the Krogan Scout. After a cutscene, you are left behind and have to find an alternative route.
The only path left is through the ruins. Jump over a gap and head into the tunnel. There are no enemies inside. Go down the stairs into the first room, and either jump through the gap off the ledge on your left, or go down the next set of stairs to your right. In the second room, there is a door to your right and to your left. Go through the door on the left, and on the right hand wall of that room is an Ancient Krogan Artifact, which you can Salvage for Credits. Return to the door on the right, go down the stairs. Jump down the ledge at the end of the path and turn to the left. In the far end of this area, you can Salvage another Ancient Krogan Artifact on the wall. After retrieving it, go to the other side of the room and turn left into a tunnel where you'll find the final Ancient Krogan Artifact on the right. Further along the path, Examine the Ravager corpse.
Head up the stairs into the light. As you move forward, you'll have to kill some Reaper forces. Then when you move forward again, a second set will drop from the sky. Once the area is clear, move ahead and turn right to jump over the gap. A wave of Cannibals will appear followed by some more coming around the corner, and finally a Brute or two accompanied by some Husks. The second wave is triggered by leaping over the gap. After the second wave, go forward, around the U-turn, and up the ledges on the left. At the same time, a third wave of Reaper forces will attack. Once they are dead, head for the right side of the open area and toward the krogan statues.
Upon reaching the second bridge, Kalros appears and chases the convoy, damaging the bridge in the process. Jump over the gap and go straight ahead. As you approach a small bridge, enemies will attack. After some more dialogue with the convoy, more Reaper forces attack. Once they are dead, you will find an SMG Scope Mod on the left side of this area. Head down and back up the two short sets of stairs where the enemies came from and find an Assault Rifle Extended Barrel Mod on the left. Turn right and drop down off the edge of a series of ledges toward the dunes to trigger a cutscene. If Wrex is alive, there's a Paragon Interrupt Opportunity towards the end of the conversation.
Clear out the two sets of Cannibals immediately following the cutscene. When you're done, go up the flight of stairs. At the top of the stairs, pick up the M-5 Phalanx heavy pistol. When you attempt to cross the bridge nearby, the Ground Assault Reaper blasts the bridge and Shepard falls down below. The Reaper targets you and begins firing its laser. Take cover frequently, and move up between the shots. To reach the Maw Hammer Controls, you must avoid getting crushed by the Reaper's feet. A large shadow will appear over the spot where a leg is about to come down. The Brutes spawn continuously until both Maw Hammers have been activated, so just run between them and ignore the adds.
After the cutscene, you speak with Mordin/Wiks. If in ME2 you destroyed Maelon's Data, Eve will be dead. There are then several possibilities, depending on what you've done thus far in the game. At this point, Shepard may either let Mordin go or stop him to sabotage the cure per the Dalatrass' request. There are multiple outcomes to this conversation:
There are several possibilities for War Assets, depending on what you chose above:
Several cutscenes ensue, including a dream sequence. Explore the Normandy to get everyone's reactions. Diana Allers will want an interview.
The following places are or will soon be available to explore:
Aethon Cluster: Aru, Esori, Nura, and Satu Arrd Systems
Attian Beta: Hercules and Thesus Systems
Bypass the door to continue. Opening the second door, take out the Guardian looking the other way, followed by all his buddies. Once clear, loot the Recon Hood on the left hand side of the wall under the big screen. In the bathroom to the left, find the M-76 Revenant assault rifle and open the Locker nearby for some Credits. Examine the dead C-Sec officer. There is a Medical Station on your way to the next room, where you'll need to kill an Engineer. Take him out, and jump into the room to grab the Sniper Rifle Extended Barrel Mod on the shelf. There's also a Weapon Bench if you want to change your loadout.
Shoot the latch protecting the Elevator Controls and Activate it, then get on the elevator to ride it up to the next level. In the next area, there won't be anything to shoot here so just pick up the loot. The first room on the right has a Pistol Piercing Mod and a Terminal of Bailey's Log. In the second room on the right, Use the Door Control computer to unlock a door behind you, in a room opposite where you found Bailey's Log. Inside you'll find the M-358 Talon heavy pistol and a DataPad with an email implicating Executor Palin. In the second room on the left are the Securitel Helmet and a Pistol High-Caliber Barrel Mod.
Go back to where you found the Door Control to exit this area. On the way out, be sure to Salvage the Account Detail Terminal for some Credits. On the other side of the door you'll find two more preoccupied Cerberus soldiers. Take them out and enter a café area. In the kitchen to the right is a Medical Station and a DataPad with Credits. You can also hear a looped transmission on the TV. Move forward and a few Cerberus troops will attack. To the right you can find another Medical Station and a Sniper Rifle Piercing Mod.
Up the stairs against the back wall, you'll get a cutscene, during which one of several things can happen:
Whatever the outcome, you wind up in a firefight through the Presidium Commons. Next you'll have to take a running-jump to a new section, where all manner of opposition awaits you as you fight your way forward. You'll eventually come to a "sealed" door. Jump the wall to your right and then keep heading up towards the Nav Point. After you jump across a smoldering catwalk and hop up a ledge, you'll find a DataPad with Credits to the left. Go through a narrow hallway opposite and drop into another open area. Kill the Atlas and Cerberus troops, then go up the stairs to the left and through the door for a cutscene.
As the adjacent elevator cars approach, you can shoot the Power Conduits to avoid fighting their occupants. Otherwise, fight off enemies until you come to a cutscene. You get some options for resolving the ensuing standoff:
Stage 1) To get Ashley/Kaidan to trust you, and thereby survive this encounter, several things are noteworthy. If you romanced Ashley/Kaidan in ME1, but romanced someone else in ME2, she/he will take some more convincing. If during the Mars mission you repeatedly insisted you're no longer with Cerberus, it'll be easier. It'll also be easier if you took all three opportunities to visit her/him while she/he was in the Hospital. And it'll be easier if you managed to save the Salarian Councilor. Using an Interrupt to tell your squad to lower their weapons when you get the chance will also make it easier.
Stage 2) When you explain that Udina is behind the coup, Udina dismisses the claim. When the Asari Councilor tries to stop Udina from unlocking the door, Udina pushes her down and aims a gun at her. Either Ashley/Kaidan -- or you through a Renegade Interrupt -- will kill Udina.
Stage 3) If you didn't use the Interrupt, and the Salarian Councilor was killed earlier, Udina will attempt to frame you for the Councilor's death. If Ashley/Kaidan does not automatically trust you, a Reputation check will be required, and if it's not high enough, Ashley/Kaidan will instruct Udina to get the door, at which point either you must kill Ashley/Kaidan with a Renegade Interrupt or a squadmate will take the shot instead. Then you will automatically kill Udina and say goodbye to Ashley/Kaidan.
On the Citadel, you can do the following:
Use the Mass Relay and go to Perseus Veil: Tikkun System, and Dock with the Geth Dreadnought. Tali is a mandatory squadmate for this mission, unless she died in ME2, in which case Admiral Xen will guide you through the mission via the radio, and you'll choose both of your squadmates. Be sure to allocate Talent Points for Tali. Enjoy the cutscene.
Make your way through the ruins of the docking tube alone. Your boots have magnets on them, and there will be several places where you'll have to walk "up" the walls. There are also two view points along the way. Once inside, proceed to the left to grab a Shotgun Smart Choke Mod, then climb back up the ledge and go around the other way to get to a ladder directly across from where you came in. Once you have climbed up the ladder, go right and through the door. In this new airlock pick up the Geth Data to the left for some Credits, and your goal is up another ladder on the right. Use the Docking Controls, and a cutscene will play. Pick up the Arc Pistol heavy pistol before continuing. Turn around and follow your squad directly behind you.
Move along the linear path, grabbing GARDIAN Defense Data and a Sniper Rifle Enhanced Scope Mod, then Activate the Bridge Controls. Eliminate all Geth and move forward and down a ladder. You will find more Geth troops at the bottom. Once they have been eliminated, move along the path and through the door, but be careful advancing: there are Trip Mines on the floor. They can be shot to cause premature detonation, but they blend in pretty well and are hard to see. Salvage more Geth Data before passing through the next door, which leads to a room with the Archon Visor in it, plus a couple of Consoles you can discuss with your squad. The room beyond it contains the Geth Pulse Rifle assault rifle. Finally, you will arrive at the Operations Center, where you have to kill several more Geth.
Once everything's dead, move out, being wary of trip-mines. Grab the SMG Scope Mod and Salvage some Geth Data for credits before Activating the Target Console. Tali will inform you that you need to get to the drive core to accomplish your mission. Tali will then open the maintenance tubes and Geth will flood inside. Eliminate the hostiles and proceed to the back left of the operations center to enter the maintenance shaft. Bypass the door, then go around left to go down the ladder. Continue around and drop down a second ladder. Salvage the Geth Data on the left, and go down a third ladder. Finally, pick up the Med-Kit and head through the pair of doors into the Main Battery.
Every time the main gun fires, an electromagnetic shockwave will come screaming along and will disable your shields unless you're in cover. Two waves of Geth will appear the moment you enter the corridor. When it's clear, a small ramp to the left has some Geth Data you can Salvage for Credits. A little further ahead on the left, Activate the Maintenance Override. A cutscene puts you inside the main gun itself. Run to the opposite end, because it'll fire again soon.
A cutscene puts you in another hallway like before. You'll immediately be engaged by the Geth. Clear the area and advance to a dead end. Take the ramp on your left and go through two doors. Around to the right is some Geth Data to Salvage. Move onto the platform and Access the Platform Controls to trigger a cutscene. In the middle of the cutscene you'll have about two seconds to control Shepard. Run forward toward your squad before the platform collapses completely, and they'll help you up. Proceed up the ladder, loot a Med-Kit, and go through the door to enter the drive core. A cutscene will be triggered, where you meet Legion or the Geth VI, depending on whether the former survived ME2.
Grab the Assault Rifle Precision Scope Mod behind you and Salvage more Geth Data on the opposite side of Legion/GethVI, then take either the platform or the ladder up to the top. If you took the ladder, move around the outside to the Data Core Override. Use the Data Core Override to free Legion/GethVI, who will then shut down the dreadnought's drive core. Multiple enemies will filter in shortly afterward. Eliminate all hostiles and proceed back around the half-circle balcony to get to the ladder down. Approach the middle of the room to trigger a cutscene, then go through the door to the left. There are no more enemies to engage, so just run through the only way you can until you approach Legion/GethVI. Doing so triggers a cutscene. During the next conversation, you'll have an Interrupt Opportunity, the morality of which corresponds to the dialog choice you make.
On the Citadel, you can do the following:
Again, Tali is a mandatory squadmate for this mission, unless she died in ME2, in which case Admiral Xen will again guide you through the mission via radio, and you'll choose both of your squadmates. Upon arrival at the Reaper base, your squad will be attacked by several Geth hostiles. Eliminate them and proceed down the hill. Once you near the bottom, the large blast door will close and three more Geth Troopers will drop down to impede your progress. Make short work of them. Check the right side of the blast door for an SMG High Caliber Barrel Mod.
Move to the right of the blast door near the tubes and vault up them. Climb the ladder on the right and eliminate the Geth Trooper waiting at the top. Vault onto the pipe and move forward. Eliminate the Geth here, then move along the right side to their position. Eliminate the remaining Geth. Pick up an Assault Rifle Piercing Mod and the Kassa Fabrication Gauntlets along the way before climbing up to the next level.
Eliminate the Geth in this next area. Once all hostiles have been eliminated, press forward and through the doors. Salvage the Reaper Tech on the right for Credits. Proceed up the ramp and destroy the lone Geth Trooper. A blast shield will expand over the Reaper tech broadcasting the signal. At the junction, go to the left to pick up an SMG Ultralight Materials Mod and head back towards to other direction. As you move along the only path you can, numerous hostiles will attempt to impede your progress. Near the start of the walkway, look for an Assault Rifle Stability Damper Mod on your right. Once all hostiles have been eliminated, Legion/GethVI will ask if you need assistance. On your way to the next door, grab the Geth Plasma shotgun and Salvage the Geth Data.
Move through the door, Salvage more Data and loot a Med-Kit. Proceed through a second door and a Nav Point will pop up. Geth will filter in from the left and the right. Eliminate all hostiles before Activating the Door Override. Geth will filter in from the left side again. Once all hostiles have been eliminated, proceed to the next Nav Point and Activate the Door Override. Legion/GethVI will inform you that you cannot double back, but you can use the elevator marked on your HUD. Move towards the elevator, but be ready. When the elevator lowers, a Geth Prime will be riding it. Eliminate it and its companions that ride down before boarding the elevator. There's a Med-Kit to the right of the elevator.
Ride the elevator up to the next level and be ready for a fight. There's a Geth Spitfire heavy weapon straight ahead, and two others to your left and to your right. After eliminating the three Geth Primes, proceed to the Nav Point. You will pull the laser designator from your back. Designate the target by holding down the trigger and making sure that you stay outside of the blast zone, marked by the blue circle. Note that the target is in front and below you, and not where the objective points. Once designated, the Normandy will proceed with its bombing run. The explosion knocks you and your squad off the upper platform, and a Reaper begins to climb out of the pit.
Legion/GethVI tells Shepard that it has acquired transport. Run to the Geth ship. You will get on top and man the turret while the squad gets inside with Legion/GethVI piloting. With the ship on the move, target the Reaper off to the left of the ship. When it goes down, you alone stay back to target the Reaper. You can only hold down the trigger when you're not moving and when the targeting circles appear over the Reaper. Prioritize dodging the incoming beams. If the Reaper hits you, it's game over and you have to start over. As you hold down the trigger, some faint blue lines will converge from either side of the Reaper. If you need to dodge, the lines will very slowly move apart again, so you don't have to start completely over again.
To summarize: spend a couple seconds "shooting" the targeting laser, dodge the Reaper's beam, repeat. Hit the Reaper four times and it'll die. The only autosave occurs after the first hit. For the fourth one, the Reaper will be very close, and the action will go into slo-mo. Despite the danger, just stand still and "shoot" the targeting gun to win.
You'll get a cutscene during which you have several dialog choices, and each will have a corresponding Paragon or Renegade Interrupt Opportunity. Once this is done, Legion/VI will appear. It wants to upload the Reaper Code to the Geth Collective. Tali/Shala'Ran doesn't want that. There are two scenarios: peace between both races or choosing one or the other.
Peace for all: Thre is only one way to make peace between the two races. You will have to pass several checks:
Choose one: If you don't pass the checks listed above, you will have to choose one race or the other. Your first dialog option is to allow the upload, or to let the Geth die. By making either decision, Tali/Shala'Ran or Legion/GethVI will protest, respectively, and a second decision is opened: allow the upload again or stop Legion/GethVI. Here are the options:
No matter what happens, explore the Normandy and talk to your crew. If Tali is alive, she'll be in Engineering behind Adams.
Liara is required to be in your party. Javik makes a great squadmate for his comments on the artifacts later in the Mission. In the first area, find the Umbra Visor and Supplies worth Credits to the right, away from Lieutenant Kurin. This is your only chance to pick these items up. Talk to start a cutscene, then get on the nearby Turret to the right of the barrier. Brutes appear in the distance, but the more immediate threat is the Husks to your left attacking the barrier you're tasked with protecting. When the area is clear, there's another cutscene. Upon regaining control of Shepard, proceed across the bridge.
When the area is clear, the far side of the bridge looks like a dead end, but the path is visually blocked by a wall. Continue forward to the end of the path and turn right. Proceed for more Reaper troops, as well as Spore Pods. Halfway across the area, you can pick up two Med-Kits: one on the right and one on the left. After clearing more enemies, go to the far left to pick up an M-560 Hydra heavy weapon. I recommend using it on the upcoming Banshee before mopping up her companions.
Walk along the path while Salvaging the Terminal for some Credits, and then Bypass a door. A camera prompt will appear for a Reaper in the not-too-far distance. You'll also see three Cannibals in the courtyard below, with their backs to you. Just to the right of the Cannibals is a Broken Shotgun that can be Salvaged for Credits. Directly above on a small ledge is a Med-Kit and Shotgun High Caliber Barrel Mod.
Make your way over to an Asari Sniper on the elevated area and get the Med-Kit, Sniper Rifle Concentration Mod, and M-98 Widow sniper rifle before approaching her. Now take out as many enemies as you possibly can, including the Barrier Engine on the wall opposite you. Once the coast is clear, proceed down the ladder, then go straight ahead through the hole in the wall, then go to your left.
After the cutscene, kill the Reaper troops. There is an M-560 Hydra heavy weapon at your feet for the heavier enemies, including a Banshee. After you clear the area, continue straight forward up the rubble and then to the right. Near the Spore Pods is an Assault Rifle Extended Barrel Mod. Past them are more Reaper troops. You don't actually have to kill the Harvesters, as they'll eventually retreat. Continue forward and around to the left to find an SMG Heat Sink Mod.
Enter the temple and pick up a Med-Kit near the entrance. The scientists' bodies are lying on the ground near a large statue, which is the artifact you're looking for. However, before investigating the statue, search the temple for other artifacts to learn about the Asari's history. If Javik is with you, he elaborates upon their history, arguing with Liara. Investigate the large statue behind the altar to receive the task of Examining all the other artifacts again. When you've activated the Beacon, you'll enter into a conversation. Kai Leng shows up and you get to fight him. When you get his shield down to half strength, he'll call in a gunship to cover him while he recharges. This happens three times before he runs out of recharges. Just take cover during the recharge. He'll run away when his shield finally runs out, and you'll get a cutscene returning you to the Normandy.
Liara will be in Javik's room, and the two will be arguing. After the argument, go back to her quarters to comfort her. Or not.
On the Citadel, you can do the following:
Once inside, you'll find a Medical Station to the right by the door. At the windows on the leftmost side there is a point where you can talk about the view. Nearby is a Log you can Examine with security footage of Sanctuary. In the cubicle farm there are three Audio Logs, a PDA, and an Inventory Log to Examine. Proceed down the stairs nearby, and you'll find two Audio Logs to the left of the crashed shuttles. In the lobby to the right there are a few Cerberus Troopers to get rid of.
When they're dead, pick up the Pistol Scope Mod next to a dead Cerberus soldier in front of the raised desk, then continue through the doorway to the left. A console will have a recording of Miranda/Oriana. After watching it, Salvage the Wall Safe behind you and continue through the opening. You'll come to a large ornamental pool that doubles as a water processing facility as well as a backdoor into Sanctuary's inner facilities. You can't miss it. Use the Water Pump on your left to drain the water, then head down the ladder and through the door on the other side. As you reach the second chamber, Salvage the Equipment and pick up the Rosenkov Materials Shoulder Plate to the left of the next door.
Continue on until you get to a room and are told you need to turn on the power. To do so, Activate the Console in the middle of the room and enjoy the cutscene. In the next room there is a PDA log on the left and another Console you'll want to Activate in the corner on the far end, which shows Miranda/Oriana again. Go down the stairs and open the doors, but be prepared for a lot of Husks. In the next room, there are two Logs you may listen to. The room after that is a long hallway stretching to the right, divided lengthwise. Kill the Reaper forces here.
Move on to the other side of the room and down the stairs. You'll enter a room where there is a Med-Kit and two more Logs from Henry Lawson. You will see another Banshee behind a window, but it can't get to you, so ignore it and go through the door on your right. There's another console with a recording of Miranda/Oriana. To your left, you can pick up Research Data for some Credits. There is also a PDA here. Head up the stairs towards a two-door hallway filled with Reaper troops.
Once you're done, go to the raised right side of the lab area to pick up the M-12 Locust SMG and a Shotgun Blade Attachment Mod, then to the left side for more Logs and a PDA. At the far end and on the left, there's another Console with a recording of Miranda/Oriana. Climb up the ladder you just lowered. Up the stairs is another double-hallway fight. When the area is clear, head down the hall and you'll enter a room almost identical to the last but without any enemies. There is a Medical Station by the door you came in. Salvage the Research Logs on the left for some Credits. Play the Log on the Husk Tanks. Go across the walkway to your right through the doors and jump across the gap. There's a Power Box on the floor in front of the tank you're standing on. Shoot the panel off and Activate it. Jump off when you're at the other side of the room and go through the door. Time to fight again.
Once you've cleared the room, there's a Med-Kit on the left side of the hallway. Head to the other side of the hall, and on the left is a Hologram Pod Control that you can Activate like a PDA. Use the "Pod - manual override" option and then turn around and the pod to your left with the Husk in it will be useable. If you don't have it already, inside is the M-99 Saber assault rifle. At the end of the hall is more Research Data for Credits, Go to the right, where you'll find an elevator. On the other side you get a cutscene. If Miranda is present, she'll be here. Start the conversation by asking about Henry Lawson's legacy: the camera will focus on the cracked glass behind him. (Hint!) There are several potential outcomes:
Miranda ALIVE and LOYAL:
A) If you pass the Reputation check, you'll be able to use a Charm/Intimidate option, which gets Henry to release Oriana. Miranda will kill her father via biotics and both she and Oriana live.
B) If you broke off a romance with Miranda she will die, regardless of her Loyalty and your warning her about Kai Leng.
C) If you denied her access to Alliance resources during your third meeting on the Citadel, or if you never met for the third time on the Citadel, she will die.
Miranda ALIVE and NOT Loyal:
A) If Miranda is present, she'll kill her father, but her father will also kill a non-Loyal Miranda, even if she was warned about Kai-Leng.
A) If you pass the Reputation check, you'll be able to use a Charm/Intimidate option, which gets Henry to release Oriana. If so, you'll get a Renegade option that allows you to kill him, and Oriana will survive and disappear from the game.
B) If you can't pass the Reputation check and "just want Oriana", you'll have a Renegade Interrupt Opportunity to wound her in the leg, distracting Henry. Shepard can kill Henry with another Renegade Interrupt. Otherwise, Shepard will tell Henry to run away, letting him go.
C) If you don't take the Renegade Interrupt, Oriana will backpedal towards the glass and throw herself and her father down, which ends in both of them dying.
After the cutscene, you'll be back on the Normandy. Explore the ship and talk to your crew.
Go to Horsehead Nebula: Anadius System, and Dock with Cronos Station. EDI is a required squadmate here. You may want to take your love interest along for comfort, as you'll learn some things about Shepard on the station. After the cutscenes, you'll land in a firefight.
Your next step is to head to the left side of the room and go up a ladder to the balcony. Do this quickly, as there is a time limit from completing the battle and disarming the hangar venting sequence from the upper level terminal. You'll loose the game and have to restart this part if you don't get there in time. Up on the balcony, there's nothing in the little chamber to the left, so turn right and head through the door. After the cutscene, you'll have to fight your way around to the balcony on the other side of the room to Use the Rotation Controls.
Look for a Medical Station in a dark room opposite to the Rotation Controls Console. Go through the next sets of doors, then, before heading down the ladder, go through another door to find a PDA with Credits. Take the ladder down and Use the Clamp Release to your right. Admire the boom, and then kill the troops and the Atlas.
Hop the wall in front of the hole and then before taking the door on the left, be sure to pick up the M-37 Falcon assault rifle. Once you've gone down the ladder, kill some more Cerberus troops. Once you've cleared out the zone, find a Medical Station and Salvage a Terminal for Credits on the far side near the ladder you need to climb. In the next room, you will find the first of four Cerberus Video Logs, which give you information on what Cerberus has been up to lately. Finding all four will net you an Achievement. The Serrice Council Greaves are directly behind you when you regain control of Shepard.
Once you're done with this first Video Log, head out and into the burning section. There'll be a drop, after which you should turn right for another firefight. When the area is clear, go up the ladder for the second Video Log. Go through the door, find a Medical Station, and Salvage Credits from a PDA. Once through the next two doors, go across the hall, ignoring the glowing blue hole in the wall to the left. Go through the two doors on the right to find a Med-Kit, the Delumcore Overlay and the third Video Log. Once done, backtrack to that blue hole and jump down.
On the other side of the drop, you will find the remains of the Human-Reaper Larva from ME2. If you destroyed the Collector Base, only its heart will be present; if you spared it, much more of it will be there. You must now fight your way up the catwalk surrounding the larva's corpse. If you chose to turn Legion over to Cerberus after its acquisition during the Reaper IFF mission in ME2, it will appear here as an enemy. Furthermore, if you did not complete Grissom Academy: Emergency Evacuation in this game, Jack will appear here as an indoctrinated foe. Both characters will then need to be killed.
After going up all three ladders, turn around away from the door to find a Med-Kit and some Credits on a PDA. Through the door, you'll reach two long hallways. The first is broken up by computer terminals and has a Med-Kit, a PDA with Credits and the fourth and final Video Log (This one is hard to see, as the targeting brackets don't appear unless you're aiming right at the keyboard area of the console). The second path leads up a ramp to the Illusive Man's inner sanctum, and a revealing conversation. Use the Investigate dialog options if you want to open up the Paragon and Renegade Persuade Options. You will need to do this now in order to have this option in your next conversation with him.
You then get to kill Kai Leng. This fight is similar to the previous one, in that he recharges his shields regularly. When he does, he'll call a few minions to help him. Concentrate on wiping out the other enemies before returning your attention to the boss. After he's defeated, there will be a Renegade Interrupt Opportunity as Leng sneaks up on you and attempts to stab you. If you do use it, you'll block the blade, shattering it. If you don't use the interrupt, you'll dodge it. Regardless, Shepard will end Kai Leng once and for all.
You will then have a last conversation with the Prothean VI with an option for a Renegade Interrupt. If you skip it, a Paragon Interrupt will present itself. Skipping both ends the conversation. Finally you will return to the Normandy.
Here are the possibilities for the final choice, dependant on your Effective Military Strength:
After you clear out the landing zone, you'll get to advance up to the remains of the second story of a building. During the cutscene, Cortez will crash. If you haven't talked to him during the game, he dies. At the top you'll fight off more hostiles. At the far end of the house is a Med-Kit and two M-920 Cain heavy weapons, one of which you need to use to knock down the AA gun. The other you should use against a Banshee and her horde. If Morinth survived ME2, this Banshee is what became of her. Survive long enough for a shuttle to come pick you up. When it arrives, ignore the remaining enemies and run to it. A cutscene plays, at the beginning of which you'll have a Paragon Interrupt Opportunity. You'll then arrive at the Forward Operating Base.
Head down the ladder onto the street. Spread throughout the base you will encounter and have the opportunity to meet however many of the various squadmates who have survived to this point. Directly across from the ladder is James. In the next building down on this side of the street is a DataPad. Across the street from there is Ashley/Kaidan. Through the door behind her/him is the Communications Tech Officer. You may ask him to speak to several living squadmates and crew via a vidcomm terminal. When you're ready to continue, go up a ramp made of rubble to the left of the Comm Room door. Talk to Primarch Victus and Garrus, if he's alive. While talking to Garrus, be ready for a Paragon Interrupt Opportunity. You cannot return once you pass through this door, so be sure you're ready.
A cut scene plays and then you get to kill some Reaper forces from a Turret. You'll automatically dismount when the attack is finished. Through the next door is Liara and two Med-Kits. Nearby you can listen to the first half of a radio conversation. There is DataPad just through the door to the right. After you've read it, approach the doctor again to hear the last half of the radio conversation.
The next door is again one way, so be sure you don't want to come back this way. Inside is Javik and Wrex/Wreav, giving speeches you can listen to. If you sabotaged the Genophage and Wrex is the krogan leader, Kirahe or an STG Officer will be found at the same spot, giving a speech to Salarian ground forces instead. During your conversation with Javik, you will have a Paragon Interrupt Opportunity. His conversation will vary depending on his relationship to Liara.
Through the final door you will find EDI, a Med-Kit, and Anderson. Depending on whether you chose the Geth or the Quarians at the end of Priority: Rannoch, a Geth Prime or Tali/Shala'Raan will be here. If you somehow managed to get both the geth and the quarians, then just the quarian representative will be here. You can overhear three short conversations between Anderson and Major Coates before talking to anyone. Talking to Anderson means you're ready for the final push. You get to make a speech to your squad, then you'll get to pick your final squadmates and make final loadout adjustments. If possible, bringing your love interest will provide a special moment later on.
Clear out this apartment, then loot two Med-Kits: one in the bathroom, and the other under a corpse outside the bathroom. You can also Examine a Computer in here. Husks will attack when you open the door. Kill the enemies in the street, and more will appear from inside the building as you approach. When the rooms are clear, there is a Med-Kit on a shelf in the back. Once you've made it through this store, jump back out onto the street. Continue catty-corner across the intersection to the restaurant on the opposite corner. Clear out the enemies lurking there.
Through the door in the restaurant's back dining room is a Medical Station. Finally you get to head out into the back alley. You'll be drawn down a long corridor which is remarkably empty. At least, until two more Brutes come smashing out through the wall. Take them out, and then go through the hole they opened, where you can find a DataPad. Going through the door triggers a cinematic.
There are two missile trucks here facing a Ground Reaper. The stores to the sides of the rear truck have Med-Kits in them. The store to the rear-left also contains an M-560 Hydra heavy weapon. Save it for the second round. First, clear out the enemies already here, then Access the rear truck's Controls. You'll then need to hold off the next wave of Reaper forces while it calibrates. Once the zone is clear, the missiles will fire but miss. You'll need to wait for the forward missile truck to calibrate. The Reaper itself moves a bit closer, and in the next round of fighting will fire its beam at you. If you decide not to seek refuge in a shop, you'll need to dodge the beam like you did on Rannoch.
The Banshees are the biggest threat. When they appear it'll be time to use the M-560 Hydra. Revive your squadmates quickly. There's no reason to save MediGel any more. Your goal is simply to survive long enough for the missiles to come online. The enemies are infinite, so when EDI tells you it's ready, stop fighting and run to the truck to Activate it.
There are several conversation branches with associated Reputation checks. In order to use the final Paragon/Renegade conversational options with the Illusive Man, you must have used a lot of Paragon/Renegade options on him at every other opportunity in the campaign, including the meetings on Mars, Thessia and the Cerberus base. The Illusive Man shoots Anderson once, mortally no matter what. The trick is to prevent the second shot.
If you are able to choose the Paragon option, the Illusive Man will realize that he is indoctrinated and then commits suicide.
The Renegade option will offer you one Renegade Interrupt. Neutral dialogue will give you two. Not taking the final Interrupt, whichever branch you choose, will result your death, and you'll have to start over. Using the Interrupt, you will kill the Illusive Man before he can take the second shot.
If Anderson doesn't get shot the second time, you get a conversation with him before he dies. The next cutscene takes you to the top of the Citadel, where you meet the AI behind it all. It takes the form of the boy you've been chasing in your dreams. Ask it everything you can, and it then gives you four options for the fate of the Galaxy. Explore them all. What's available is dependant on your Effective Military Strength. Refusal remains an option regardless, and will be triggered immediately if you choose any of the lower-right options, or you leave the conversation and you turn around and shoot the hologram.
Here are the consequences of your choice:
A DataPad screen then appears with a thankyou note from the game's developers. Clicking the only button will put you back on the Normandy, with a save just before going to the Cerberus Headquarters. Why? I suppose so you can try one of the other endings.
last modified 7 April 2018