After your victory on Tuchanka, head to the Citadel to inform the Councilors of your victory. As Joker tries to summon the Citadel for landing permission, he will find that nobody is at their positions in the Comms Station. The reason will become clear soon enough; Thane will contact you, if he lived through Mass Effect 2 (otherwise it will be Commander Bailey,) with reports of Cerberus invading the Citadel. As you fly through the Citadel, you’ll see scenes of war and chaos all throughout the facility. When you land, you will be thrust immediately into the action.
Cerberus will wipe out most of the guards in this initial area, and with Commander Bailey sitting wounded at the far end of the room, it’s up to you to kill the invaders and reach the Commander. First things first, kill the Combat Engineer at the far end of the room. He will have already set up a turret, and you don’t need him making any more. Snipe him from afar, or use your squad to do so. There are several “lanes” leading from your location to the back of the room, almost like a bowling alley. Using these lanes, close quarters soldiers like Sentinels, Vanguards, and Soldiers can funnel the enemies to create choke points. Use Garrus to set a Proximity Mine in one of these lanes, or Liara to cast Singularity and Warp, or simply use Nova if you have it, in combination with a Shotgun. As you wipe through the enemies, command your squad to focus on the turret from afar. They probably won’t be able to destroy it as efficiently as you would, but they’ll at least keep the turret off your back while you move through the lanes wiping out the remaining Cerberus troops.
When the battle is over, speak with Bailey by the door. He will open the C-Sec door for you and tell you about the situation. Thane, if he is alive, will have left the hospital and gone off in search of you. Ashley or Kaiden will have left the hospital to protect the Councilors. The salarian Councilor is off by herself, probably in the Executor’s office, as Garrus (if he’s there) will suggest it as the most defensible position in the Council. Go around to the left or right to leave the C-Sec offices and pass through the lobby.
Two soldiers will be in here with their backs turned to you. Quickly kill them to avoid alerting them. The soldiers in the next room to the left won’t be so easy to bypass, however. Seeing their friends go down, they will begin to fire into the lobby. This battle will demand a bit more thought than the last ones. A shielded Guardian will come down the stairs, while several others will wait at the top with a Combat Engineer. Wait for the first Guardian to come down the stairs, then pop out and either shoot through the slot in his shield or hit him from behind. You can try using a Combat Drone on the Guardian to distract him, them open fire on his exposed back.
Several more Guardians will be at the top of the stairs. You can lay an ambush for them at the bottom of the stairs by setting a Proximity Mine on the stairs, or by using the Scorpion to set makeshift mines on the walls. If one of the Guardians hesitates and lowers his shield, using Concussive Shot or Carnage to kill them almost immediately. A combination of this tactic and the Pull ability is especially effective. With the Guardians dead, rush the Combat Engineer at the top of the stairs. He may have spawned a turret already, in which case you will have to take cover and whittle the turret down before finishing off the Combat Engineer. Use Biotic Charge to close the distance, or gun him down from mid range with an Assault Rifle or SMG.
Search the counter to the right at the top of the stairs to find the Assault Rifle Piercing Mod and a med kit. After this, another wave of enemies will come dropping down from the ceiling. Open fire with an Assault Rifle and you will be able to kill most, if not all, of them before they hit the ground. Finish off the stragglers. Head to the next room. Examine the terminal and the Cerberus corpse to learn more about the initial attack. In the next room, you will find a Guardian with his back to you. Snipe him or otherwise eliminate him before he can turn, or before your overzealous squad can turn him on to your presence. Two Centurions and a Combat Engineer will emerge. Charge after the Combat Engineer first. He will retreat to the back of the room on the right and attempt to assemble a turret. Keep shooting him to ensure that he doesn’t have time to assemble the turret. From here, you can exit through the back of this room and flank behind the two Centurions. Before you leave this area, be sure to collect the various items scattered about. You can find the Recon Hood on a counter to the left side of the room. Head through the left-hand door to reach the bathroom. Here you will find the M-76 Revenant Assault Rifle and some credits inside of a locker. Examine the C-Sec corpse to get some commentary from your squad, then leave the restroom and search the Medical Station by the back exit of the room. When you are ready, leave through this back exit to reach a hall with a window on the left. A Combat Engineer will be trying to hack a console to unlock the elevator. Shoot him in the head, then climb through the window, shoot the lock on the console, and activate the switch inside to open the elevator for you. Collect the Sniper Rifle Extended Barrel Mod on the shelf next to the switch and head into the elevator.