The Shelter is an abandoned Cold War-era fortification built by the U.S. government and was sold to a fanatical militia group. The group later converted the Shelter to be used as a research facility for various scientists and militia members, with the goal of artificially evolving humans into ANMC creatures that stuck to a strict caste system. Additionally, the Shelter acts as a housing and command center, transport system to the outside, and a gateway to Neo Ark. Very little is known about the militia that ran the Shelter or what involvement the U.S. government played in its construction after selling the original property.
The first area of the Shelter encountered is the entrance area past the door near No. 9's motorcycle in the last room of the Abandoned Mine. This area consists of a long hallway, where Aya Brea will battle the Ivory Stalker, followed by a small platform and an elevator. Taking the elevator at the end of the platform takes Aya to the Shelter's B1 level.
This level contains the Armory, the Sterilization Room, the GOLEM Freezer, a parking lot, and the living quarters. The B1's Main Corridor consists of a raised catwalk with six rooms, four at the sides and one at each end. The level is important for housing the armory, where Aya can purchase items, weapons and ammunition, and the sterilization room, which has a save point and a lift to descend to the Shelter B2.
The B2 level for the shelter contains almost the same layout as B1, but is important because it also houses the elevators that can take Aya to Neo Ark. The B2 level consists of another raised catwalk, but this time over water, populated by Bog Divers. Other than this, it contains the Laboratory, the Examination Room and the Breeding Room.