WARNING: The point of no return is during this quest. I would suggest finishing any achievements or side-quests you need before speaking with Sarah Lyons.
Speak with Sarah when you're ready to finish the game. You will head outside and follow the giant robot from the Citadel back to the Jefferson Memorial. Again enter the Gift Shop door and head to the Rotunda where the control room for Project Purity is located. Colonel Autumn will be waiting for you. With a high speech skill you can convince him to step aside. Otherwise, just kill him. However, the control room is now completely irradiated and is about to self-destruct.
You have three options now to finish the game:
Sacrifice yourself or Sarah to enter the room and activate Project Purity. The code for the console is 216.
Inject the FEV virus into the water filter.
Do nothing and let the place explode.