Vault 46 would be a social experiment, what would happen if the vault had a murderer? It would be showing paranoia, seeing how the dwellers would react if a murderer was hiding amongst them? Scientists would be place just behind the vault, to monitor. There wasn't actually one, however, after 10 days of the vault door closing a dead body would be placed in the cafeteria. This would instill paranoia, what if their roomie was the cold-blooded murderer? Was it the cat? After a couple of days, another body would pop up, the body was a highly popular dweller at the time. It would make the dwellers realise that the murder was killing people fast and they really needed to do something quick.
The overseer would then be forced to set up a type of government that would work to try and find any traces of the murderer. The next body came yet again soon later, but this time... There would be some DNA left over. One from a leader of the government. Automatically, the dwellers were in outrage. There was no way he would have ever been caught in the act, what if the other government leaders were working with him? The leader was soon executed, the rest of the leaders jailed in a cell.
For a while, the overseer had been sitting back as to not want and ruin the experiment. The population had other ideas. A couple of days later, as everyone was relaxing - enjoying that the murderers were locked up or dead - another body was found. The peacefulness had ended. The dwellers soon were questioning the overseer. He wasn't even talking about the incident! Has he even left his office? This led to an infight with the dwellers and the overseers security. However, some were on the side with the dwellers so they stormed with them to the overseers office and killed the overseer.
Even more killings happened. Soon, it became too much. Everyone started fighting, they knew it was someone who was pulling the strings... But who? The fighting continued until there were only 15 people left. 3 groups appeared, the "Freedam", "Savers" and "Investigators".
In the end, the 3 groups started a mini war. Only 1 person from each group survived. The scientists had thought for a long time, but unlocked the vault door. The 3 survivors all left, not even looking back.
The scientists would create a vault of themselves with the free space since the dwellers left. Eventually, it looked as if the scientists had always lived there. No one knew the horrors of what happened back then, and it'll remain that way.