Raven Rock (Enclave base)
We look around the room and grab all our belongings from the locker on the right. We exit and immediately run into a guard who tells us we can't move freely around the base. Using our speech, we convince him to talk to the president and find out why he gave us freedom, and then we proceed. If your speech isn't up to the task, you can simply kill him. It won't make any difference; the entire base will be hunting us in a couple of minutes anyway.
Our first target is the biolab on the second floor. You'll see maps on the walls, marking sectors. Upon entering, immediately turn left and climb the stairs. Of course, you can wander around the rooms a bit more and examine the experimental results more closely, as that will soon become very difficult.
On the second floor, we immediately turn left, and Colonel Autumn will countermand the president's order over the intercom and order you killed. That's when the fun begins. We move forward, clearing the area of Enclave soldiers. Turn left, eliminate the soldier below, and, going a little further, descend the stairs. Don't forget to navigate along the way using the maps hanging on the wall. They clearly indicate the sectors and the routes to them. Once in sector 2B, go through the doors and down the corridor to the lab. Descend the stairs and head to the next sector, 2C.
As we move down the corridor, don't forget to check the side rooms for ammunition and medical supplies. In the room on the left, we'll find Anna Holt, the former assistant of Dr. Lee and our father. We speak with her and learn that she betrayed Project Purity and all of us, telling everything she knows to the Enclave. You can kill her or leave her alive; it won't affect the story at all.
Meeting with the President of the Enclave
Eventually, we reach a spiral staircase and climb it. There's a large computer in the room; it's President John-Henry Eden. We talk to him and discover he's not such a bad guy after all. However, Colonel Autumn is gradually spiraling out of control, and it's becoming increasingly difficult to control him. We inquire about the Enclave's plans and learn that their scientists have invented a virus that can wipe out all mutations on Earth. Simply add this virus to water purified by Project Purity, and all mutated creatures will die. The only downside is that they will also kill people who were only lightly affected by the radiation, and they're not as dangerous to society. If your speech skill is high, you can convince Eden to blow up Raven Rock (the Enclave base) along with everything in it.
After the dialogue, we take the vial containing the virus and exit through the door that opens. Before we reach our long-awaited freedom, we'll have to wander the corridors a bit more. Robots will come to our aid and do all the dirty work for us. Just before the exit, we'll be attacked by two Enclave soldiers armed with Gatling lasers. We kill them, loot their gear, and head out.
Outside, we witness our old friend Fox fighting Enclave fighters. It turns out he's come to our aid. We offer him a ride, and if our karma is positive, he'll agree.
All that remains is to return to the Brotherhood of Steel Citadel and report the current situation. There, we witness a meeting of the Brotherhood's top brass. After listening to them, we report that the Enclave has stolen a G.E.C.K. and demand action. Guardian Lyons will speak with us and inform us of our new title, along with a gift of two sets of armor to choose from: power or recon. We choose the appropriate one and complete the mission. The final mission remains .
Source: SSoHPKC
See also:
Fallout 3: Companions (Part 1)
Fallout 3: Tempenny Tower
Location Map (with bobbleheads)