When you have fended off the initial attack on the Presidium, head down to the far right and drop down. Proceed to the left and pick up the credits on the ground on your way around the edge of the building. Climb up onto the next floor when you reach the end of the path. Run forward and past the Snap, Crackle, and Shock Defense Solutions store on the left. As you pass this area, more Cerberus troops will emerge, championed by an Atlas mech.
In this battle, you can choose to either hijack the mech, or turtle up and slowly defeat it. The former is clearly the more appealing option, but may not be plausible if you miss a few shots or are taking too much damage. If you can, equip your Sniper Rifle and shoot directly at the cockpit, right at the soldier inside. You should see the glass begin to crack. When it finally breaks open, shoot the pilot with one more Sniper Rifle round and climb into the Atlas mech. Swing around to bring the full force of its cannon and missiles down on the enemies behind you, mostly Assault Troopers.
If taking the Atlas mech for yourself is not a viable option, head inside of the Snap, Crackle, and Shock store that you passed earlier. This room is basically a square, and you can take cover under the window in the front right-hand corner to avoid the mech’s fire and pop out to quickly shoot a few volleys back. You may also want to command your squad to take cover on one of the planters outside of the store, because if all of the Atlas mech’s attention is focused in the store, it will quickly flank behind you through the store entrance and then you will have to find a new position.
When all of the enemies have been defeated, proceed to the end of the area and walk up the stairs to the left. Open the door at the top and run to the elevator to see a short cutscene of the assassin, along with a few Phantoms, closing the elevator door and riding up to intercept the rest of the Council. Shepard will jump into the elevator shaft and land on top of another elevator, which Bailey will control remotely and send speeding after your enemies. As you ride on top of the elevator, you will have to fend off several waves of enemies riding the elevators to your sides. First, though, you will have to shoot the power nodes on the bottom of the assassin’s elevator, which will be located on the bottom of it, right above you. Look up and shoot both of the grey boxes to slow the elevator down.
The first group of attackers will come up to the left of your elevator. Switch to a Shotgun if you have one. Otherwise, be prepared to use charged melee attacks and crowd-control powers such as Singularity, as well as heavy damage-inducing powers like Incinerate. Keep your distance from the Phantoms and wait for them to either focus on your squad-mates or charge you. At close range, they are easy fodder for your Shotgun. You can avoid this combat altogether if you are fast enough by shooting the power nodes on the Phantom’s elevator as soon as it comes into view. This will cause their elevator to drop before any of them can make the jump over to yours.
A few seconds later, another elevator will rise next to you, this one on the other side. A group of Assault Troopers will fire at you from this elevator. Again, look for the power nodes on the elevator and shoot them to send the Assault Troopers plummeting to their deaths. If you can’t hit it on time, simply take cover behind one of the mechanical systems on your elevator and return fire. Use a Grenade or Singularity and Warp together to take out the group, as they will be clustered together on the small elevator. Take out the rest with an Assault Rifle or SMG. Two more Assault Troopers will jet down from above you. Quickly switch back to the Shotgun or used charged melee attacks to kill them. You will have to leap over to the elevator next to you now, so jump the gap and watch as a cutscene plays.
Kaiden or Ashley will be with the Council in the elevator, but hearing your landing on top of him, he assumes you to be an assassin and fires up through the roof. When the elevator reaches its destination, he will shepherd the Council out of the elevator and to the dropship they were going to use for escape. It will be in flames. Sheperd will drop down from the elevator, gun drawn. Udina gives the command to kill you, as he claims that you will have been working with Cerberus to initiate the attack. Kaiden or Ashley will hesitate.
At this point, you can hit LT to perform a Paragon action and command your squad to lower their weapons. Doing so will increase your chances in the upcoming conversations. Your old partner will question aloud your past allegiances with Cerberus, wondering whether or not you can be trusted. Whether Kaiden or Ashley does trust you depends on a number of factors, including: How often you visited them at the hospital, whether or not you saved the Council in the first Mass Effect, whether or not you romanced them in the first Mass Effect (and if you did, whether or not you romanced someone else in Mass Effect 2,) whether or not you spoke with him/her on Mars about his/her reservations about your time with Cerberus, and finally, whether or not Thane lived in Mass Effect 2. If Thane did not live, Udina will produce edited security footage that he has put together of you attacking the Councilor in the Executor’s office, who will have died since Thane was not there to save her. If you can’t gain Kadien’s or Ashley’s trust, you will have to shoot them. If you can, he will lower his weapon. Udina will insist upon opening the elevator, which you all will say holds Cerberus assassins, and none of the other Council members can stop him. You will get a Renegade option that will make you shoot Udina, stopping him from opening the elevator doors.
When the elevator opens, Bailey will emerge and say that he chased off the Cerberus assassins. If you managed to get through with Kaiden or Ashley alive, congratulations, you have just earned yourself a new party member.