In Mission: Humanity the human race and most of it's colonies have been enslaved, destroyed and drained of its resources by alien aggressors. After a struggle, however, humanity is able to free Earth from their clutches and aquire their technology. The remaining Humans who have survived the inital alien invasion decide to band together and hunt down the rest of the alien race to prevent the same fate befalling any other species. In addition to hunting dow the alience menace the player is also allowed to colonise new planets from which Humanity can begin to prosper from once again. The player is to assume command of Humanity's last hope and save themselves from extinction whilst stopping those that nearly destroyed us in the first place.