The Colony is the home of Mother Sphere and members of the Airborne Squads and EVE Protocol after the Final War.

It is, in fact, a massive cluster of machinery designed in the vein of a Jupiter brain/swarm that orbits the planet. There are many Colonies that are integrated into this structure. Originally designed for humans fleeing the Human-Naytiba War and the Final War, it was revealed that Mother Sphere had no intentions on letting the humans use them as refuge; this is shown in the Colony Extinction, where Mother Sphere dropped the Colony that the humans were using onto the planet, destroying it in the process and causing the devastation seen in all areas of the game.

Various sidequests shed more light on how life in the Colony works. Mother Sphere is seen as a god and savior, as she creates all Andro-Eidos artificially and oversees every aspect of the Colony. Andro-Eidos do not eat; instead, essential nutrients come in the form of a liquid paste which is simply ingested through tubes. Everyday life seemingly revolves around Mother Sphere, construction of weapons and maintenance of facilities/vehicles like Providence, and Airborne Squad training to take out the Naytibas on Earth. Mother Sphere seemingly rewrote the history of Earth, claiming that the Naytibas were of unknown origin and leaving out that the Andro-Eidos she creates are in fact designed to replace the original humans, not save them. She also seemingly leaves out that they are different from humans in general, as well.

While not elaborated on, all Andro-Eidos born in the Colony seem to have their memories uploaded to Mother Sphere upon death. Whether this is true or not remains to be seen, as well as what Mother Sphere actually does with these memories to begin with if they are.