Vault-Tec Corporate Vault

Vault-Tec's Secret Vault was a place of the company's private Forced Evolutionary Virus research located under the ghoul town of Los.

History
Like many major military contractors, as Vault-Tec grew in finances and responsibility, it began to develop highly experimental and secure technologies. In time, Vault-Tec was so thoroughly integrated with top-secret military research, it was practically a division of the U.S. government - almost. The company still retained some elements of privatization. So the principals of Vault-Tec - executives, scientists, and so on - had to be aware of the true function of the Vaults, and they had access to the technology. They were the developers. Regardless of the U.S. government's directives, Vault-Tec was not going to submit to a lottery and live underground with a bunch of human cattle in facilities that were intentionally defective. Thus Vault-Tec created their own facilities, removed from the larger Vault network - and kept secret from the U.S. government.

Vault-Tec didn't stop there. These secret, private installations were used to research the latest vault mechanisms as well as technologies that would benefit mankind in a post-nuclear environment. This, of course, included some extensive research with FEV.

No one can say for certain how Vault-Tec obtained FEV. Some think they had it all along, gaining it in a deal with the government, others think it was stolen from the government while VT was repairing one of the more guarded vaults.

After the defeat of the Master, part of his army remained together, under the command of a visionary lieutenant named Attis. Highly intelligent and vindictive towards the Brotherhood of Steel, Attis took his group into hiding, searching for clues regarding the history of the FEV virus. Learning about a secret Vault-Tec installation with new and possibly improved versions of the FEV virus, Attis led his group to the area where the rumors started, the ruined city of Los. His ultimate goal, of course, is the continuation of The Master's plan - to rebuild the mutant vats and eventually transform the entire human race into mutants.

Appearances in games
The Secret Vault appears only in Fallout: Brotherhood of Steel.

Inconsistency
Judging from what is known from Fallout and Fallout 2, all FEV research was conducted either at West Tek or Mariposa and it is highly unlikely for Vault-Tec to have obtained it. However, Fallout 3 establishes that not only did Vault-Tec know about FEV, they had a huge stockpile of it in one of their Vaults, so this becomes far more plausible.