The vault's original purpose in the vault experiment is unknown. Recently, due to Reese's experiments in the vault, it has become a veritable jungle with huge mutated plants that thrive there and will provide more than minor obstacles to overcome.
The player character would have had to fight their way through the mutant plants as the ecology desperately tried to kill them. Once at the third level, they would have found a G.E.C.K. and a key. On a desk, papers including bios on Banshee and the Jackals and a map showing the origin of the Nursery documenting Reese's movements southwards as well as his next destination, Austin, could be found. Using the key to drive the car away from Vault 39 would have ended Act II.