To destroy them, one can choose to kill every member conventionally; hack Paladin Ramos' security terminal (Science of 75 required) to set the bunker turrets to target Brotherhood members; or get the three keycards from Elder McNamara, Head Paladin Hardin and Head Scribe Taggart to initiate the bunker's self-destruct sequence.
To have them enter a treaty with the NCR, Still in the Dark must be completed and McNamara be Elder (having not been replaced by Hardin during the quest). Telling McNamara that the NCR wants them destroyed will prompt him to offer Colonel Moore a truce, which she will accept.
You cannot work for both Yes Man and Colonel Moore for this quest. If you get "You'll Know When It Happens" from Yes Man before you get it from Colonel Moore, then you will be forced to play the rest of the game as a Wild Card rather than working for the NCR. In this case, Colonel Moore will ask you to protect President Kimball, but Ranger Grant will not respond to any attempts to talk, therefore, The quest cannot be completed. An easy way to avoid this is to ignore Yes Man completely, therefore preventing him from giving you the quest before you actually want it.
Sometimes you can walk around the counter to Grant and he will initiate conversation about protecting the president even if you received the quest from Yes Man before the Colonel.
Completion of The House Always Wins IV (or higher) will result in this mission being failed. Note that if you have already completed How Little We Know when you turn in The House Always Wins III then part IV will automatically completed and you will fail this mission.
When speaking to a member of the NCR, they will mention Colonel Moore has accepted the Brotherhood of Steel's offer to aid them in battle, even if the player has not yet spoken to her about it.
This section is needed but has not been written yet. You can help The Vault by writing it.
PCPlayStation 3Xbox 360 If you talk to Regis about his opinion on NCR the objective "Talk to Colonel Moore about a Great Khans/NCR alliance" is added, however there is no speech option with Moore regarding this.
PCPlayStation 3Xbox 360 Killing Mr. House using the sterilize option causes endless notifications to appear of Wild Card: Change in Management's "Return to Yes Man".
PCPlayStation 3Xbox 360 Upon completing How Little We Know without speaking to Liza O'Malley in the NCR Embassy, For The Republic Part 2 will continuously say that you need to report back to Colonel Moore about killing (or creating a treaty) with the Khans. However you cannot talk to Colonel Moore upon returning to Hoover Dam.
FIX: type setstage 136166 10 in the console - quest will be started over, but will just talk through the dialogue trees and be able to continue the quest as normal.
FIX: Alternatively, use these console commands to fix the bug. They must be entered in this order: SetObjectiveDisplayed 136166 30 1, SetObjectiveCompleted 136166 30 1. If you foiled the Omerta's plans: SetObjectiveDisplayed 136166 35 1. If you helped the Omerta's plans: SetObjectiveDisplayed 136166 36 1
PlayStation 3 Sometimes completing Oh My Papa while Wild Card: Side Bets is active will not complete the Great Khans portion of For the Republic, Part 2, even if the Great Khans have agreed to help the NCR in the coming battle.