Those who survived near Chicago formed a new Brotherhood chapter, different from the original Brotherhood, on their more liberal ideology, founding Bunker Alph in 2187. The two that remained, though badly damaged, managed to drift across the planes before they crash landed one near Chicago, the other just south of Kansas City, practically on top of the super mutant camp. Over the Rocky mountains the fleet hit a terrible storm, destroying two of the four ships. The dissenters were collected and sent on a mission to the east aboard a fleet of airships to track down the remnants of the Master's Army.
After a dispute about sharing technology with and even recruiting outsiders, the High Elders finally decided that the Brotherhood would survive as it always had in its shroud of secrecy. The Midwestern Brotherhood of Steel is descended from the original West Coast chapter, and was the first chapter of the Brotherhood to 'go native' and seperate from the primary organization.