As a control Vault, Vault 3 stayed unopened until a water leak occurred, forcing the residents to open the Vault and search for assistance. Running a trading program, all went well for the inhabitants until the Fiends set their sights on the Vault for a new headquarters.
Since the Vault residents had set up no security, the Fiends needed little effort in raiding the Vault. The Fiends burst through the entrance sector and massacred every single resident in sight, putting the Vault 3 population into extinction. The Fiends had then occupied the Vault, and set up their new headquarters inside.
The New California Republic turned their attention to the Vault, and sent a lone ranger into the Vault with the task of killing Motor-Runner and exterminating all the Fiend personnel inside. He was injured and broke his leg in the fighting, and the events afterwards are uncertain. Depending on their actions, the Courier could have come along and assisted Anders, and then proceeded to eliminate Motor-Runner and all the Fiend personnel inside the Vault, permanently fracturing the Fiends.
The Raid of Vault 3 is mentioned only in Fallout: New Vegas.