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You can make it here by completing New San Francisco quests #2, #3 and #11. After that, you'll have to enter the tanker in SF north of Chinatown, head on up to the bridge and tell the ship to "go." You'll then be dropped off at the gates to the Enclave, somewhere off the California coast. Congratulations on making it this far.
Your main goal is to descend a few levels, get the Presidential Access Key from the President, descend one more level, shut down the reactor computer, and then make it back up in time to defeat their leader, Frank Horrigan. After he's defeated, you can then escape. Along the way you can help rescue your tribe from Arroyo, held captive one level below. You can accomplish all this the diplomatic sneaky way, or the more difficult and time consuming mass destructive way. The choice is yours, but I'll outline the major tasks involved and let you decide.
When you enter the Enclave foyer from the Dock, you'll find yourself in a large room. This is the room where the final battle takes place. Take note of the computer terminal along the southern wall, and of the turrets lining the wall. Take a minute to save your game, use the computer, log in as J, Smith and see what you can do (save your game first just in case)... and you'll find out that you need a Presidential Access Key to handle any of the security measures. That's fine, because that's what you'll want to get later in the Presidential Area from the man himself. Log off.
To the east of the foyer is the Barracks, but take the south stairs from this room into the Detention cell area. It's a rather large area and you enter on the north. Your goal is to make it to the spiral stairs on the south, that lead to the Access Corridor. If you're still lacking in equipment, be sure to thoroughly search all the lockers and bins on this level... and when you head south to the cells, you'll find your Arroyo tribes people there, including the Elder. Both she and the man in the cell across from her can talk to you about what you need to do... namely shutting down the reactor and finding another GECK (even though you may have one still). Fortunately, another GECK can be found in the Access Corridor, so take the south stairs.
This level is a maze full of 9 square cells, each with a computer terminal and a door on every wall. As you make your way through the cells, the floor will shock you. Read on for how to fix this (though by then it's not really necessary). Probably the easiest way to describe this puzzle is with a small matrix. For this analogy, the cells will correspond to the numbers on a phone pad:
1 2 3
(a) 4 5 6 (b)
7 8 9
Each computer terminal in every room opens up different doors, and your goal is to start from room #2 and make it to room #0 at the bottom. Both side rooms (a) and (b) contain valuable items. In (a) you'll find Advanced Power Armor MK II, the best armor in the game, along with a lot of other potentially useful equipment, and in (b) you'll find the GECK along with other valuable stuff. To open up the door to #0 you'll need to be carrying a GECK. In room #9, you'll find some disconnected wires. You can repair these (with a tool) to stop the periodic electric shocks along the floors. Here are some phone numbers:
2, 1, 2, 3, 3, 8, 9: to open all the needed doors including the side rooms (a) & (b)
2, 1, 4: quick access to both (a) and (b), but then you'll need to re-use the sequence below:
2, 3, 1, 7, 8, 9: quick way to #0 without using the side rooms
When you've made it past the door to #0, head down the south stairs to the Presidential Area.
You're almost there. On the east central side of the level you'll find the President. If you want to avoid an extremely tough fight at the end of the game, it's crucial that you get his key. You can talk with him and learn all about their plans, but end the conversation without threatening to kill him, else he'll call all the guards on that level and you'll have a fight. The easiest way to get his access key is to either use 8 Super Stimpaks on him in succession, wait 10 minutes using your Pipboy and take his key off the ground, or use sneak and kill him with one good shot (save first).
When you have the Presidential Access Key, head to the northwest room with a scientist named Dr. Curling. If you can pass your Speech checks with him (and it's not too difficult), you can convince him to release the FEV virus into the ducts. Tell him he can take his time and that it's a difficult concept to swallow. He'll inject you with an antidote and release the same antidote into the cells where your tribes people are as well. This is completely optional by the way and will eliminate one avenue of shutting down the reactor. However, the other method is even easier so don't fret. Here's where the fun begins. Exit the Presidential Area by "using" the stairway to the north of the President's room.
Welcome to the reactor area. There are two ways to shut it off. One is by threatening the scientist named Tom Murray in the southwest corner and getting him to do it. You can only do this if you haven't already released the FEV virus into the air. The second way is even easier, especially if you've released the FEV. Wait 10 minutes on your Pipboy so that all the scientists and civilians explode from the FEV, enter the mainframe room on the northeast part of the level where you'll find three terminals. If the scientists are still alive, you can wait until they move around and give you access to the front of one of the terminals. Step in front of any of them, arm a stick of dynamite and drop it in front of the terminal. When it explodes, you'll have successfully shut down the reactor and gain a nice chunk of (probably unneeded now) xp. Head back up the same stairs to the Presidential Area.
Since the way back up through the Access Corridor is blocked now (after shutting down the reactor), find the southern spiral stairwell in which the small room's previously closed doors are now open to you. These will take you to the Barracks.
Make your way to the northwestern exit grid and into the Enclave area again... but when you arrive, stop and wait for instructions.
After entering this area from the Barracks, you'll notice a small antechamber with about four Enclave soldiers. One of them is Sgt. Granite. Talk to him, and after he tells you about Frank Horrigan, tell him it "sounds bad." Tell him that unless he helps you defeat Frank Horrigan and get to your ship, all of your chances of survival are non-existent... or something to that extent. He'll agree to help you in your assault in the main foyer.
Enter the foyer carefully and when you see the central floor insignia, step carefully to the south part of the room. Your objective is to walk along the south wall to the computer terminal without triggering the dialog from Frank Horrigan. This is not an exploit, as the game gives you some room to make it there. For fun, before you access the computer console, save your game (which should be done regardless) and walk up to Horrigan to initiate conversation. Listen to what he has to say and attempt to beat the game with both the turrets and Frank firing multiple times at you. Incredibly tough.
After you've had your fun with Frank, reload the game and access the terminal. Access security measures and then initiate counter insurgency measures using your Presidential Access Key. The turrets (and Sgt. Granite's team) will now be focused on Frank Horrigan. You should get away scott free after this, but do your part in shooting Horrigan to make him go down faster as he's got a ton of HP. When he's almost dead, he'll drop to the ground and say something to you on your approach... something to the effect that he's activated the self-destruct mechanism and you'll all die miserably. It doesn't matter, you'll be long gone when you exit the door. Open the door, exit and witness the nice ending cinematic as well as the various endings for the towns and areas you've traveled to. Congratulations!