Once you return to the Citadel, you get a response from either Thane or Commander Bailey. So pick your squad and get ready into hot water!
Bailey under fire[edit]
You start by taking down Cerberus troops. Also take out the turret left by the Cerberus Engineer. As soon as the room is clear, talk to Bailey as he reveals in a computer reception about the councilor meeting and execution. So pretty much go through the rooms field with Cerberus troops, shields and things you'll encounter along the way. Once you reach the room at the end after taking the first elevator to the top, a cutscene kicks in. Now if Thane isn't here, the salarian councilor gets killed, but if Thane is here, he saves the salarian councilor.
Council countdown[edit]
After the crash of the shuttle car, you start at the Presidium. Follow along killing not just Cerberus troops, but also ninjas as well! There's a middle section on the right to cross to another section. When you reach there, take care of the Cerberus Atlas and the remaining ninja troops. Once that's over. Go to the elevator. Kai Leng beats you to it so you take the other elevator in the cutscene. The idea as you go up the elevator section is to aim at the two electrical parts to get more experience, but take to long and Bailey takes over only once. Do the same with the next elevator but on the top. Then the bottom again on the third elevator. Then jump to the fourth elevator for a tense standoff.
Kill or not to kill?[edit]
At this point, Udina is trying to escape and convinces Ashley/Kaiden that you are with Cerberus. Now if the salarian dies, it shows you killing the salarian councilor saying "You're going to pay for this!" But if the salarian councilor lives, it won't be shown at all. Also as a key moment. If you didn't meet Ashley/Kaiden between each mission in the hospital, you'll be forced to kill her/him. So make sure you do if you want to save her/him from the standoff. Then kill Udina to end the sequence. After the aftermath in talking to Commander Bailey, if Ashley/Kaiden isn't shot by you, you can let her/him stay or join you on the Normandy. The choice is yours if you're deciding on the squadmate.