And so the traitor's plans of power were ended. But the Brotherhood remained in danger. With the NCR forces closing in on the Hidden Valley bunker, Elder User opened the door to the Elder's chambers and called for a meeting. Head Scribe Chaucer was given the job of restoring the brotherhood's files for proof that Aeroscribe acted alone, and of the Brotherhood's actions to catch him. However, the hacker, T0ad impeded these efforts for a time, but he was caught within a day and given the same punishment as the traitor. The delay still allowed the NCR to reach the bunker before negotiations could be made with the NCR.
As the NCR prepared to break through the bunker's door, the Elder ordered Head Knight Senpai and all remaining Paladins and Knights to hold back the soldiers while a connection was established with President Kimball. They held off the soldiers, but without the Head Paladin to lead, there were many casualties on both sides. The connection finally went through, and soon the NCR fell back as the order to cease fire was given.
The NCR had never been known for being lenient, but President Kimball showed some degree of mercy, at least compared to destroying all of the brotherhood then and there. The Brotherhood was forced to move East, out of the NCR territory.
Without any place to call home, the future of the Mojave Chapter of the Brotherhood of Steel was unknown. But for now, the Brotherhood still stands.