There'll be a room where two Enclave soldiers are up above and behind you on a platform, so be careful when you reach that part. Take out the Ghouls along the way and you'll finally reach the Brotherhood's hideout. Head up the ladder and Dr Li will get you into the Citadel and the end of the mission.
Missions 10, 11 + 12
Picking up the Trail / Rescue From Paradise / Finding the Garden
These missions have been bunched together as they all intertwine and you'll complete them almost without realising one after another. Now you are inside the Citadel you can do a variety of things such as: getting Power Armour training, getting a Brotherhood of Steel member to follow you for the rest of the game and the next location that you need to visit. So head over to the opposite side of the courtyard and into the Laboratory where you'll find BoS member Star Paladin Cross who will join you if you ask her to. Speak to the head honcho Lyon and get permission to trade and to also get Power Armour training from Paladin Gunny outside in the courtyard (this allows you to wear BoS and Enclave armour for MUCH better protection)!
Now head to the Vault-Tec terminal in Citadel A Ring and then speak to Scribe Rothchild for information on the location of Vault-87. Follow him to the glowing map and then head outside to the courtyard. It's quicker to fast travel to Smith Casey's Garage (aka Vault-112) and then follow the marker to Little Lamplight and head into the caverns.
You'll run into a little runt at a barricade and if you don't have the Child at Heart Perk or a high enough speech skill, you'll have to head to Paradise Falls and get the children out. Follow the pointer on your map to Paradise Falls and you'll now have a variety of ways to enter the town. You can either:
1). Start the sub-quest 'Strictly Business' and capture the 'slaves' that you're asked to capture (gaining you negative Karma).
2). If you have a high enough speech level and a total of 1700 caps you can bribe your way in and buy the kids from Eulogy.
3). Kill every slaver in Paradise Falls and get showered with loads of positive Karma (however, if you kill everyone here you'll no longer be able to complete the 'Strictly Business' quest and thus miss out on its Achievement). So we recommend that you create a save file here and try out option one (for the Achievement) and then option three.
Option one is covered later on in the guide (so skip to that part if you want to do it now), or simply go in guns blazing (ideally with your BoS partner), kill the slavers and then rescue the kids (be warned that you'll need a fair bit of health and ammo to get through them all)! Once the kids are outside the gate you'll complete mission 11, so fast travel back to Lamplight and re-approach the barricade.
The Mayor can now be persuaded to let you in, so enter and then talk to the mayor again until he guides you to Murder Pass. Once the gate is open, make your way through the door, but have enough ammo and health ready for the Super Mutants that lie up ahead.
Once you're inside the Vault, you'll need to wade through a decent number of Super Mutants (of all types) and you'll eventually come across a Mutant trapped in a test room. If you help him escape, he'll get the G.E.C.K. for you, but you'll need to shoot your way through a few monsters to get back to him. Once Fawkes is out, follow him (killing any Mutants in the way) and he'll retrieve the G.E.C.K. device for you. Leave him and head back the way you came until you're suddenly stopped by a blinding ball of light...
The American Dream
You'll wake up trapped in a cell with Colonel Autumn interrogating you for the Purifier Code. Tell him where to go and he'll be told by the president to leave you alone. Once you're free grab all your gear from the locker (and re-equip it all) and head out. You're supposed to have a free passage through to the president, but as that'll get halted later on, you might as well kill your way through now!
So make your way to level two of Raven Rock (killing all in your path) and you'll eventually come across 'The President'. If you stopped off in the Colonel's room earlier on this level, you'll have the energy weapon Bobblehead and the self-destruct code (found in the footlocker). Tell the president you know the code, take the virus and head out through the level one door. You'll be attacked by the Enclave, but there'll be sentry robots to help you out now. Once you make it outside, you'll meet up with Fawkes again, so head back to the Citadel for the final mission...