Late-game research uncovers the truth: the invasion is being orchestrated by the , a highly advanced, psionic race that has enslaved other species to serve as their military arm. Their primary base in the solar system is located in the Cydonia region of Mars. The Final Assault: Cydonia

As the Commander, you start with basic human ballistics while fighting various alien species, such as the physically frail but psionic and the brutish Mutons . The "story" is largely driven by your research:

The modern XCOM: Enemy Unknown reboots this story for a new timeline. In the timeline of XCOM 2 , it is revealed that X-COM actually lost the war early on, and the "victory" from the previous game was a simulation run in the Commander's mind while they were held captive.