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.
The ultimate goal is to destroy the Alien Brain , a massive bio-computer that serves as the mastermind and central hub for the invasion. The Endings UFO: Enemy Unknown
Once X-COM develops the (a powerful interstellar craft), they launch a final mission to Mars. The modern XCOM: Enemy Unknown reboots this story