You will receive a message from Jacob Taylor, provided he survived the run to the end of Mass Effect 2 (otherwise, a generic soldier will take his place,) and he will provide you with an interesting and potentially lucrative arrangement. He, and a group of other Cerberus soldiers and scientists, will not be happy about the way that Cerberus has been running things lately. Appalled by the rampant violence on display in Cerberus’ latest actions, Jacob has led the rebelling scientists to the safety of a facility of Arrae, where they will ask that you help them in return for them lending their talents to the Crucible project. To this end, you will spend most of this mission attempting to turn on the anti-air guns on the facility’s roof.
As you land, it will be immediately clear that the scientists are in trouble. Heavy Cerberus numbers are present at the landing pad. Take cover behind the crate at the drop zone and open fire on the Shield Generators to the right and left. Once they are destroyed, you will have an easier time taking out the Cerberus troops here. Pick them off from afar using Assault Rifles or SMGs in case a few brave soldiers get too close. You can also choose to simply run into the battle, using the Shield Generators to power yourself up while you work at the enemies with a Shotgun. This strategy works well for Vanguards and Sentinels.
Head to the main gate after defeating the initial wave of enemies to speak with Jacob and Dr. Brynn Cole. She will tell you that she and her fellow scientists split away from Cerberus after finding out that the scientists in Cerberus’ employ were slowly disappearing. Apparently, Cerberus has a policy of killing their scientists after they complete their tasks, for fear of them knowing too much valuable information. As the Cerberus troops begin their bombing run, Jacob will tell you to get to the roof and start up the AA guns.
Speak with the various scientists in this room, then head past the locked door to find the Assault Rifle Magazine Upgrade. Climb up the stairs and collect the Medi-Gels from the Medical Station on the wall, then proceed to the infirmary and talk to Cole and Jacob one more time. If you pursued a romantic relationship with Jacob in Mass Effect 2, this conversation will be all the more interesting. Check the console on the wall to get 2,500 credits, then examine the Medical Station for either Medi-Gel or experience. Pick up the Kassa Fabrication Greaves on the crate by the entrance to this room, and the Turian Toxin Data in the larger lab room. Finally, grab the Shotgun High Caliber Barrel Mod by the door.
When you are ready, leave the infirmary and climb up the ladder. Collect the M-6 Carnifex Pistol when you reach the top, and then proceed outside. You will come across a group of enemies near a Shield Generator, but with their backs turned to you. Shoot the pylon, kill the Combat Engineer, and take cover behind the two pipes in front of you to quickly finish off the rest of the soldiers. When the firefight is over, pick up the SMG High Caliber Barrel Mod on the stack of small boxes in the corner. Head forward to restore the satellite links. Of course, more Cerberus troopers will be laying an ambush for you here. A Combat Engineer towards the back will be your biggest concern in this battle. Snipe him or eliminate him using powers to hopefully prevent him from setting up a turret. The rest of the soldiers should be fairly simple to eliminate, provided you make good use of your squad and your powers.
Along the way to the satellite array, examine the Med Kit and the datapad on the wall and on the ground. You will collect 2,500 credits from the datapad. Examine the uplink to repair the satellites. Now that you have restored part of the AA guns, more Cerberus troops will begin to attack you. Look up to see their dropships pouring more soldiers onto the battlefield. Try to shoot them as they drop from the dropships, before they can even hit the ground. Don’t neglect the highest Assault Trooper either, though, as he will climb up to the roof and use a turret against you. Shoot him from long range, or use Garrus to sniper him or Liara to toss him away with Singularity.
After the battle, grab the Sniper Rifle Piercing Mod behind the crates towards the back of the roof. Climb up the ladders and examine the gun to activate it. Turn and head across the walkway towards the second gun. Check out the small room ahead to find the Shotgun Spare Ammo Mod, a Med-Kit, and a datapad. When you reach the second gun, you will find that you will have to assign one member of your squad to fix it while you and the other squad-mate defend them. Climb onto the mounted gun on the roof and use it to lay waste to the Cerberus troops that begin to pour in from the dropships. If you see a Phantom, one of the female assassin troopers introduced on the Citadel, take them out immediately over anyone else. If they get close, it’s game over.
Several waves of enemies will charge you, but you only need to resist and time your reloads well. Soon, the gun will be repaired. Head back and activate the second AA gun. Now return to the labs to tell Jacob of your progress. Dr. Cole will point you to a console, which you should activate. Suddenly, Assault Troopers will burst through the windows and launch a full-scale attack on the lab itself. Command your squad to take cover at either side of the room while you sweep down the middle. Catch the enemies in your crossfire to eliminate them quickly, then go downstairs and again protect the scientist from the Cerberus soldiers. When the soldiers are clear, the doors will open. Head outside as the last of the Cerberus troops descend upon the facility. Either use or destroy the Shield Generators dotting the area. Vanguards and other close-range classes may want to keep the Generators active, as they can be quite helpful when you want to rush in. Just keep in mind that if you take this strategy, Phantoms roam the area and will be more than happy to skewer you on their swords.
An Atlas mech will drop onto the battlefield, along with a few waves of Combat Engineers. Pick off the Combat Engineers to your left first; if you don’t, they will set up turrets and flank you. Either destroy the mech or its pilot, taking control of it, and wipe out the remaining turrets and Combat Engineers. When all of the enemies are destroyed, a cutscene will play and you will escape the facility with the scientists.