MAIN QUEST 13: Take it back!
Received from: Elder Lyons [Citadel - lab]
Solution: When you arrive at the laboratory you'll notice that Sarah is talking to her father. Wait for this conversation to end and talk to Elder Lyons yourself. You must inform him that G.E.C.K. is in Enclave's possession and you'll find out that Enclave forces are probably inside the Purity project chamber. Don't tell Lyons about the FEV virus you've acquired in Raven Rock, because as I said you will be allowed to choose an ending not soon from now and it would be unwise to block one of the possible variations. The Brotherhood of Steel will finally decide to proceed with the assault and obviously you're going to be a part of it. Listen to the plan and talk to Sarah Lyons. She will inform you that you've been promoted and as a result you can take a power armor set or a recon armor set. In both cases you'll receive an armor and a helmet. Take your time to put on a new armor, unless you're already using something more interesting. Talk to Sarah again and confirm that you're ready to begin the invasion (screen).
It's rather important that you listen to Sarah's plan. You can also take a closer look at the large robot which is going to be used during the invasion. It's being transported to the surface at the moment. Follow Sarah Lyons to Citadel - courtyard. As you've probably noticed, a crane is being used to transport the robot to the outside. Obviously you will have to get there in order to join the fights. Use the main gate to return to Capitol Wasteland. Don't be surprised by the fights taking place between Enclave and Brotherhood of Steel units. Sarah suggests that you should stay near the robot and it is a good advice (screen). Notice that the robot is moving towards Jefferson Memorial. If it stops, scout the area ahead and eliminate Enclave units who may block its way.
You will probably have to secure a road leading to a nearby bridge. Once this is done, go back to the front of the Citadel and wait for the robot to start moving towards the bridge. It shouldn't take too long for the machine to reach the first force field which is going to be neutralized after a short while (screen). Now you will have to be patient and continue moving slowly towards your final destination. I wouldn't recommend staying too close to the robot, because it's going to be a target for enemy artillery and you wouldn't want to find yourself in the crossfire. You can eliminate visible Enclave units, but they'll probably they anyway before you get too close to them.
Continue moving close to the robot until you've reached the second force field. Ignore the fact that the robot will lose balance for a second or two, because it'll return to full shape after a short while. Now it would be a good idea to secure the area around Jefferson Memorial (screen). You don't have to kill all Enclave soldiers, however it's recommended, so you won't have to worry about being attacked while trying to get inside the monument. Eventually you'll have to use the door leading to Jefferson Memorial - gift shop. Notice that a second quest (Project Impurity) has appeared on your list at the same time. Ignore it, because it's only a small reminder that you'll be able to get to an alternative ending. Keep reading and you'll know everything soon enough.
You'll have to be very careful inside Jefferson Memorial, because the museum is being guarded by at least TWO large groups of Enclave soldiers. There are also single enemy units here and there. I would recommend that you use your most powerful weapons to kill enemy soldiers, including the fatman (screen). The main reason is that you won't have to preserve your ammo supplies anymore, because you're very close to the end. Leave only a few projectiles in your inventory, because you may need them for the last fight. Your objective is to get to the door leading to Jefferson Memorial - rotunda.
It's EXTREMELY IMPORTANT that you save your progress before entering rotunda, because you won't be allowed to go back!
You'll be stopped by colonel Autumn once you've entered this final area. I guess you may be surprised to hear that you won't have to kill him. Instead, you may resolve this problem in a peaceful manner, but only if you've destroyed Raven Rock and if you succeed in a speech challenge (screen). If you decide to fight, get ready to kill Autumn, as well as two of his bodyguards. It's very important that they die quickly, because they're using powerful Gatling guns.
Either way, once the problem with Autumn has been resolved use the stairs to get to the upper balcony and join Sarah. Listen to a transmission from Doctor Li and you'll find out that you'll have to activate the purifier in the next few minutes or otherwise it's going to explode. Save your game and wait for Sarah to talk to you. Here's where you'll decide how to end the game...