The Project is a faction that's dedicated towards rebuilding civilization. It is the faction that the player is a commander of.
Early in the year 2086, a group of survivors fled Seattle searching for a safe haven. After fighting off bands of marauders, they discovered an abandoned base within the Rocky Mountains on April 10, 2086, and made it their new home. By 2099, the Project emerged from its military base, and by 2100, prepared to search for key artifacts that would enable them to rebuild civilization.
During the campaign, the Project sent 3 teams to recover key artifacts. Team Alpha (which the player starts as the commander) was sent to the state of Arizona in the Western Sector in order to recover the Synaptic Link technology, while Team Beta was sent into the ruins of Chicago, Illinois, located within the Eastern Sector, in search of VTOL technology, and Team Gamma was sent into a region of the Rocky Mountains located within the Northern Sector.