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After burying the scientists in the wastes outside of Mariposa, the soldiers sealed the military base, then headed out into the desert, taking supplies and weapon schematics with them. Captain Maxson would then lead his men and families to the government bunker at Lost Hills, and the surviving soldiers went on to eventually form the Brotherhood of Steel.
Although Maxson's points in his holodisk indicated that civilian personnel were to remain at the base, whether they did or not is unknown.