Over six square acres of rock was tunneled out, and like Cheyenne Mountain, was built to withstand a thirty megaton nuclear explosion. Underneath the tons of granite, the buildings were built on huge metal platforms that rested on thousands of steel springs. There are four separate towers, containing the laboratory facilities, with eight storage and agricultural buildings in the center of the hollowed out mountain. There were smaller buildings along the walls of the cavern, they were the places that made the self sufficiency possible. All the recycling and a small amount of manufacturing went on in the smaller buildings. The scientists and their assistants all lived at the facility, rarely going to the surface. There were three exits, two of which that were ever used, one tunnel ran for miles to the northeast, ending under a group of warehouses used to deliver supplies and necessities to and from the complex. Another tunnel ended in Boise, at the Capitol Mall Complex. When visitors arrived, this was the entrance they used. The last exit came out at the base of the mountain, near a trailhead and was disguised as a locked pump station. It was a forgotten emergency exit that had fallen into disuse after the Cold War ended. It was located behind the agricultural buildings, a rusted set of double doors hidden behind stacks of food crates.

The tunnels had maglev trains running back and forth several times a day. There were passenger cars and freight cars for bringing in the guests and supplies that were not grown or made inside the mountain. There was a small station for the trains, and a platform for boarding. The opposite side of the tracks had a dock for unloading supplies. The station was located at the center of the southern wall of the Complex. Smaller maglev tracks were made for carts to move supplies to the different destinations.

Nearly five thousand people lived at the complex, including maintenance and service employees. Two thousand and two hundred of those were currently being housed as test subjects. Electric carts were used for transportation, to prevent the ventilation system to be clogged with exhaust fumes. All the alternative energy sources that were being prevented from becoming mainstream were used almost exclusively. Nearly everything was recycled, composted and reused.