When you’re back on the Normandy after the Virmire mission (or whatever core mission you completed last, as the case may be), you’ll have your usual post-mission chatter, this time revolving around whichever companion you left with the nuke. Not much of consequence comes from this, and after Liara does another reading - and subsequently swoons - you’ll get the opportunity to chat with the Council. Put up with them and stick to the Paragon or Renegade options for Paragon +2 or Renegade +2, respectively.
Once that’s out of the way, you’ll be free to explore the Normandy again and chat with everybody. Honestly, however, there’s not a whole lot of new chatter here. You can talk to Garrus for a new Codex Entry, and if you saved Captain Kirrahe, you can talk to him and do some shopping with Commander Rentola, for what that’s worth.
|Secondary - Aliens: Council Races / Turians: Religion|
With that, you’re done on the Normandy. When you use the Galaxy Map you’ll be summoned back to the Citadel… assuming you’ve completed all the core missions in the game up to this point (Therum, Feros, Noveria and Virmire). Looks like the Council is finally ready to take serious action against Saren!
When you arrive at the Citadel, watch the scenes that follow and say what you will in response to Udina and the Council and, perhaps, your romantic interest who attempts to console you on the grounded Normandy. You may have been thwarted, but an old ally - Captain Anderson - may have a solution, and you’ll be told to meet him at Flux in the Wards to discuss the matter.
Final Assignments on the Citadel
Ride the elevator up to C-Sec Academy and use the fast travel terminal to travel to Flux. Before you head up into the club, however, turn around and head downstairs, then turn left towards the Med Clinic to find a crowd gathered. You’ll be hailed by one Carlos Saracino, starting the assignment Citadel: Our Own Worst Enemy. Return towards Flux and outside you’ll find a self-important pencil-pusher named Elias Keeler, who wants some drugs to help his negotiations. This starts the assignment Citadel: Negotiator’s Request.
Just a few final errands you can take care of before you plunge inexorably towards the end of the game.
|Secondary - Humanity and the Systems Alliance / Terra Firma Party|
Resolve those assignments however you wish, then head into Flux and chat with Captain Anderson. His plan is pretty straight-forward: He’ll take the bullet for you, commit a bit of treason, and free the Normandy so you can flee to Ilos. Your only choice in this matter is what Anderson’s target should be, either Citadel Control or Udina’s office. We suggest that latter, as it’ll give Udina some well-deserved comeuppance and Anderson the pleasure of administering it, but as far as the mission is concerned, both options will get you the outcome you need.
Return to the Normandy and watch the scenes that follow, and when you’re back in control on the Normandy you’ll be free to travel as you please. You can still travel around the galaxy and complete assignments, but for obvious reasons you can’t return to the Citadel, which may prevent you from completing some quests. When you’re ready to push on towards the end of the game, travel to the Pangaea Expanse cluster, the Refuge system, and land on Ilos.