Now that you have a scientist who is willing to help take down Belltower, you'll need to get her safely off the station with her evidence so Interpol can protect her.
Get Kavanagh off the base[edit]
After talking with Kavanagh, head back out to the elevator and take it back up topside. You'll contact Keitner through your InfoLink, and she'll get the coordinates to Interpol. On the way up the elevator will stop and Keitner will tell you that Burke must have intercepted your communications. You'll need to find your own way back up and through the base that is now flooded with Burke's men who are looking for you.
Use the emergency ladder switch on the side of the elevator to drop down a ladder and start your ascent. You'll use ladders and environmental obstacles to climb and jump up. At the top, if you can move heavy crates and have your legs upgraded, you can get up to a higher level where you'll receive some experience and a Praxis kit. Follow the air duct at the top around and down to the ceiling above the room where you took the elevator down. When you drop down you'll see three enemies standing guard in front of the elevator, waiting for you to come through the doors. Their backs are to you, so you can safely sneak by without engaging them. Head through the interrogation wing to the checkpoint, after which you'll run into Keitner, who will give you the coordinates and tell you that Burke is gassing the prisoners and the lab. You'll need to make it down to the circuit board below the command tower to redirect the gas. Keep in mind that you have a time limit until everyone is dead, so don't waste too much time on your way down.
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You have seven minutes before everyone dies in the gas. When Keitner dies, head out into the vertical bay where you'll see two snipers talk together. If you have the reflex booster augmentation you can take them both down at once, otherwise you'll need to wait for them to split up if you're going for stealth. There is a third sniper at the opposite end of the third floor, and he patrols back and forth around the stairs. Since he'll continue scanning the lower floor with his sniper rifle, it can be helpful to take him out rather than just sneak by him. On the second floor a couple more roving guards, and on the bottom are two more.
When you get down under the command tower, the hacker will contact you over the InfoLink and tell you to choose between killing the prisoners or Dr. Kavanagh. You can use the gas flow control to redirect the flow from one area to another, killing whoever is there and saving the other side. Alternatively, you can save both the prisoners and Kavanagh by entering the vent in the southwest wall, jumping up to another vent and disabling the gas at the source in the room beyond with a well-placed bullet or explosive. Or just stand their and let everyone die.
The last thing you need to do before heading back out into the base to find Burke is to disengage the lockdown up in the command tower. All you have to do is touch the mainframe screen, and then you'll contact Kavanagh and let her know it's safe for her to leave in a submersible for Interpol to pick her up. Go out to the security checkpoint to the rest of the base, and Burke will contact you to let you know he's on to your "Corporal Tyler" persona. He knows you want to find Megan and challenges you to get past him to continue your search. Also your play style will determine his comment on you.
Before you leave, go to Quinn's shop which is empty but unlocked. The safe's would be unlocked whether you save the prisoners, save Kavanagh, let both die or let both live. Make sure you collect it before the showdown.
Confront Burke[edit]
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Like the detention area, Burke's men are patrolling all over the base, and you have to make it all the way back through the offices and the two loading bays you've seen to the newly opened Loading Bay 3 where Burke is waiting. There are snipers, heavies and turrets everywhere, so the easiest way is to avoid confrontation and sneak through to the final showdown. When you leave the checkpoint and head into the halls, note that an enemy is facing you on a different level on your mini-map. Wait until he turns away before proceeding to avoid being spotted. You'll also receive a message from Quinn, who is leaving before he stuck on the base. If you go down to his shop, he's opened it up for you to grab some of his stuff. It's actually a good idea to go down that way anyway if you want to sneak out into Loading Bay 1. Go through the offices if you took out the wall or want to, or go around the west hall taking care not to set off the frag mines. There's one guard patrolling the middle east-west corridor, then you can take the vent down to Quinn's shop where you'll find a Praxis kit and a couple safes that will be open depending on how little blood you shed getting to this point. You can also find reload speed and target-seeking upgrades in his secret stash, along with a small weapons arsenal. Use the elevator to get back up and you'll be behind one of the enemies for an easy take-down, or just sneak behind him and take the stairs up.
At the upper door leading out to Loading Bay 1, get cover and open the door. You want to go out when you see the snipers on the office and up in the rafters above looking away from you. When they are, take the walkway up to the office and either use your jump aug to get on top of the office to take out the sniper there, or go through the office door and quickly take out the enemy there before knows what hits him. Whether you went through or above the office, continue on to the other side and down to the bottom floor where you can take the open container across to the west door. Get cover at the end of the container and when the turret isn't facing you and the guard is away, sneak by the turret and through the door. In the hallway leading to Loading Bay 2 are some more laser turrets, so carefully make your way between the lasers or use the invisibility aug to get through.
At the door to the next loading bay, get cover next to it and open them when the heavy outside is away. When both the enemy is gone and the turret is facing off to the your right, sneak out and along the east wall, disabling the frag mine on the wall behind one of the containers. Continue past the turret and take cover behind a container where you can watch a group of enemies have a conversation about you. When they break up the closest one will post right out in front of where you need to go, but when he moves to his second position you're good to hug the east wall and move all the way down to the south end of the bay. Down at this end, watch for the enemy that patrols back and forth from the turret by the exit, and when he's walking away, just walk right past the turret and into the hallway. This leads to the final confrontation with Burke.
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After Burke talks to you, a boxguard will come to life and the final battle will begin. There is cover right where you start and it only takes one well-aimed EMP grenade to disable the mech. If you're going for the Factory Zero achievement/trophy, this is really the only difficult part of the DLC. You'll need to get cover immediately and when the east sniper isn't looking, use the cover to quickly get into the bay without the bot seeing you, until you can get into the open container in the middle. From there you can sneak over into the southeast corner of the bay and take the ladder up to the top of the office and take out the heavy up there before dropping down into the office from above and taking out Burke. This is also the recommended way to get Apex Predator, instead of just shooting Burke in the face from outside the office. If you have weapons and upgrade available to you, it becomes much easier since you can take out the boxguard with a grenade and it becomes a normal gunfight. You'll need to take out all the men in the loading bay to finish this objective.
Go to Loading Bay 2's docking platform[edit]
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When the fight is over, the mystery hacker will once again contact you over your InfoLink. This time he wants you to meet him at Loading Bay 2 so you can catch the ship that's going to Megan's location. He's faked orders from Burke, so the way should be clear. Perhaps surprisingly, the hacker turns out to be Quinn and he'll give you some limited explanations for his involvement. If you have the CASIE aug, you can use it one him and although he'll detect it, it will make him answer some more questions about the larger power struggle in the world. After your conversation you'll get into another stasis pod, this time hopefully heading for the wherever they're keeping Megan and the other Sarif scientists.