Over time, the Brotherhood has been at war with the New California Republic. After the end of Fallout 2, they basically got into conflict with NCR over control of technology, mostly energy weapons, cause that's one of the main purposes of the Brotherhood, to control that technology. NCR didn't want to hand it over so they went to war. So by the time you start playing Fallout: New Vegas, the Brotherhood is really a pretty small faction compared to the NCR, so they're not a group that you see initially in the game, you hear rumors about them. Eventually most players will have to deal with them.​