Brotherhood War

The NCR and the Brotherhood of Steel staged a long and bloody war spurred by disagreements on how technology should be regulated in the wasteland. Despite having far superior technology and training, the Brotherhood has gone into retreat after having lost many battles on the front lines. The outcome of the war is best illustrated by the Mojave Chapter of the Brotherhood of Steel. After taking heavy losses in the Battle of Helios One, they retreated to Hidden Valley and have remained in exile. The NCR success can be traced to their superior commanding, such as Colonel Moore, and most notably to their far superior numbers. For example in the Battle for Helios One, they outnumbered the Brotherhood twenty to one. However, the conflict was a Pyrrhic victory for the NCR at best. Heavy losses to Brotherhood meant redirecting troops from the front lines against Caesar's Legion, and less soldiers to to protect vital caravan trading routes.

Chronology
By 2231, Jeremy Maxson had assumed the position of Brotherhood High Elder. In addition to wanting to expand Brotherhood operations eastward, he was much more aggressive in his "hoarding" of pre-war technology. He wanted to restore the power of the Brotherhood by wresting all advanced tech from the hands of "lesser people" by any means necessary. Naturally, this led to disputes with the NCR, which had always been in favor of using advanced technology for the benefit of society (at least according to Thomas Moore, an NCR citizen, which is what he saw as the NCR's justification for trying to annex Vault City). Shortly after the destruction of the Enclave in 2242, a war broke out between the Brotherhood and the NCR.

With their superior technology and training, the Brotherhood managed to hold out against the NCR, even coming close to total victory. Yet, the Brotherhood's technological advantage was eventually outdone by the sheer size of the NCR's army; no matter how many troops the NCR lost, they always seemed to have more. The Brotherhood, on the other hand, were still a selective group, and thus, were short on replacements. With this discrepancy in troop numbers, the Brotherhood's defeat was inevitable. The length of the war is unknown, although Cassandra Moore was said to have served 'four tours against the Brotherhood', so it is likely that the conflict lasted for several decades.

The Mojave chapter of the Brotherhood of Steel would still be fighting the NCR as late as 2274. After establishing a base at Helios One, the Mojave Brotherhood soon found themselves at odds with the NCR and its growing power in the region. Eventually, the NCR sought to control Helios One, and the Brotherhood, under the orders of their Elder, Elijah, refused to leave. This led to a confrontation between the two, and in the typical chain of events, the Brotherhood's superior technology was no match for the NCR's superior numbers.

Aftermath
Defeated in one of the bloodiest battles in the Brotherhood's history, in which over half of the chapter was killed, the Brotherhood retreated to the Hidden Valley bunker, where Nolan McNamara (in light of Elijah's disappearance following the battle) took the role of Elder upon himself, and placed the bunker under lock-down, stranding Brotherhood stragglers and ceasing contact with the outside world. Since then the Brotherhood's presence in the Mojave Wasteland has been confined to only a few scouting missions.

Elijah set up an outpost at an abandoned Brotherhood of Steel bunker, and later set off to the Big Empty in search of technology to eradicate the NCR. The NCR held the power plant, but were unable to get it up and running. Its lack of a proper power output later made it a low-priority target for Caesar's Legion

By 2281 the war is a stalemate because of Brotherhood's cessation of attacks and withdrawal to their hidden bunker. The Courier can only destroy the chapter if pursuing the NCR storyline and most other storyline within the game, the only option with a truce is if the player follows the Wild Card storyline, in New Vegas.