Conserning the Hanlon part- that's what you get for choosing that quest ending. Serves you right.
Same for deciding to rape BoS.
I hope all of your save files corrupt and your toilet clogs.
Seriously, check NV Wiki for the BoS quest and reload a previous save for the Halnon quest, just another one of gazillion bugs present in the game.
EDIT: Here
"You must go to the Hidden Valley bunker and enter to destroy the Brotherhood of Steel in the area. If you have not interacted with the Brotherhood, you must go through an orientation by convincing a Ranger in an adjacent bunker to leave. If you warn the Ranger in any way about the Brotherhood, the Brotherhood will become hostile and enter the bunker to kill you. Due to the last portion causing Don't Tread on the Bear! to fail and the NCR to name you a terrorist, the Ranger will not talk to you and will be hostile, so you are going to have to kill him. The Brotherhood will confiscate your weapons, so it is recommended to carry some holdout weapons before entering. If you have Veronica as a companion, then you can move more freely in the bunker.
General notes
A Brotherhood patrol will leave the bunker at night and patrol inside the fenced in exterior area of the bunker. You may encounter this patrol when entering or leaving the bunker. Regardless of how you deal with the Brotherhood, the patrol will have to be dealt with also.
If you have Veronica as your companion, blowing up the bunker or killing the Brotherhood will cause her to abandon you if your reputation with the Brotherhood drops to low. A reputation of liked will be sufficient to avoid losing her if destroying the bunker, while idolized will allow you to kill a few members while detected and still keep her. Remaining undetected while killing all of the Brotherhood results in no reputation loss and thus she will not leave or scold the player.
Destroying the bunker
Once you have access to the bunker, you need to steal 3 keycards from 3 main personnel in order to get the password for the self-destruct sequence or have a Science skill of 100, at the same time you can look for a bunker key for your escape later on. It is suggested that you save before pickpocketing each character in order to avoid killing for the keycard if they catch you stealing. You need to go level L2 of the bunker, where you can find Elder McNamara, Head Paladin Hardin and Head Scribe Taggart. Head right, where you can find McNamara, who is the easiest to steal from and can be stolen as he is sitting in his chair. Hardin can be found to the left of this room in one of the three bedrooms. He will be in the room sleeping, standing, or on his computer. Crouch, wait until you are hidden and then steal his key card. Go back towards the door to L1 and go all the way up the left hallway this time. At the end is the self-destruct room, where you will also find Taggart.
Note: If you helped remove Elder McNamara in the quest Still in the Dark, the Head Paladin keycard can be found on Paladin Ramos.
Once you have all keycards, return to the room where Taggart is and obtain the password from the Override Code Generator terminal (green) next to the actual self-destruct terminal (blue). Now use the code on the self-destruct terminal to destroy the bunker and head out of the bunker.
After activating the self-destruct sequence with the password, you will become a villain in the eyes of the Brotherhood, so you will need a good exit strategy. Here are four alternatives:
A single Stealth Boy can get you out without firing a shot or getting shot.
If you kill the scribes and the apprentice in the computer room before starting the self-destruct and put on their robes, everyone in the bunker will be friendly except for McNamara. Acquire a bunker key from someone and make your escape.
You may re-program the turrets, using the terminal in the first section of the bunker (Ramos' office). You have the options to deactivate or reset target parameters. Using the "registered Brotherhood" option will turn the turrets on the Brotherhood, yet leave the Courier alone (even in a Brotherhood disguise). To access the terminal you will need a science of 75.
Before heading up to L1 to make your exit, acquire a key from the paladins guarding McNamara. If you do not steal a key, you must attempt to pick the final door (100, very hard). Now make your way to L1. Having a lot of stimpaks, ammunition and good weapons to fight your way out.
Preserving the bunker
Simply kill all of the Brotherhood of Steel in the bunker and the night patrol outside. The quest will be updated and Caesar will act as though the bunker was destroyed. If you dress in a Brotherhood faction disguise the turrets will not shoot at you while attacking the bunker, you may also use stealth kills and silenced weapons to remove all Brotherhood presence without losing any fame.
Use of this method leaves the ammunition crate received when reaching liked status in the Brotherhood intact, it will also refresh its free energy weapon ammunition every time you exit and re-enter L1 of the bunker, despite no one being alive to restock it."
