In the late 37th-early 39th century, Jon Spectre was a member of the Clan Chosen. Roughly in the late 36th century, Apocalypse ascended to power and ruled much of North America unchallenged, for 100 years, where humans and whoever else resistant to his rule could be killed at any moment. The Clan Askani were the only rebellion left to opposed Apocalypse's rule.
Years later, following the destruction of the Askani Sisterhood, by the New Canaanites led by Ch'vayre and Stryfe, and Apocalypse, by Nathan Dayspring, Jon joined the Clan Chosen, an Askani-inspired team of freedom fighters, formed originally by Nathan, Tetherblood, and Aliya. Training in the Askani ways under surviving Askani elders, the Clan Chosen repeatedly battled the New Canaanites and the Scions of Apocalypse, led by Stryfe. The Clan Chosen also clashed with the Neo-Canaanites, a group that also wished to claim Apocalypse's power.
Traitor to the Clan
After decades of battle, the Clan Chosen signed a long-lasting peace treaty with the New Canaanites, but Nathan, upset by rumors that Apocalypse had survived, convinced the Clan's Askani Council that they needed to fight again. However, ensuing battles cost the Clan dearly and the following war nearly destroyed all life on Earth. Among the dead was Jon’s father, Adam Spectre. After Jon was accused of being a traitor to the Clan Chosen, he traveled to the modern era to warn Cannonball of the danger of Dayspring.
After convincing Cannonball of Dayspring's destructive behavior, Dayspring (known as Cable) arrived with X-Force and battled Spectre, until Cable, who was attempting to recruit Cannonball back into X-Force to fight against the Skornn, left with the remaining members of X-Force. Spectre, Cannonball, and Sunspot aided X-Force, Wolverine, Deadpool, Thing, Human Torch, and the Mutant Liberation Front in battling the Skornn.
Jon remained in the modern era and was depowered during the M-Day and the energies that he used to control were then drawn to The Collective.