The vault I added to my game was just that: a vault to protect people from the war. There was an ulterior motive, as there usually is, which was to see if a resident’s mind could be integrated into the computer running the vault, but keep their personality, memory, et all, and see if anyone noticed.
The idea was to carefully pick the resident that had the best chance of success, a guy called Tommy Wilksop, then fake his death for the experiment. However, there was a spelling mistake on the selective decision, and it ended up being Timmy Wilksop, the guy’s kid, that was chosen. Even so, the child’s mind was fully integrated into the vault’s computer mainframe and the experiment was deemed a complete success, despite some early teething issues.
Those teething problems (messages through terminals from the boy) led to the boy’s parents suspecting their child was still alive (faked his death, remember?) and they demanded answers. In a scuffle, a gun went off and Timmy’s mother caught the bullet. Being inside the cameras throughout the vault, Timmy saw his mother die. In his distress, Timmy got angry and the faculty robots bought into that rage. The resulting battle saw everyone dead. Timmy has been on his own since, for decades, and still has the mind of a ten year old.
When the pcs stumble into the vault, everything is in good condition with plenty of food, water, comfort, etc, until they want to leave. Timmy does not want to be on his own any more and tries to force them to stay. To escape, the pcs have to destroy the vault (either blow up the reactor, or wipe the hard drives with Timmy’s personality on it) or take the computer wizkid out into the surface world with them by downloading him.
Then, The Institute and BoS turned up and wanted the tech. Players have a choice to keep it for themselves (for whatever use that could be), destroy it, or give it up (for whatever consequences it could lead to). My party gave the disc to the BoS, as they had already had bad encounters with some synths.