Legion, a powerful psionic mutant on Earth and son of Professor Charles Xavier, travels back in time with the intention of killing Magneto. He believes Magneto's death will allow Xavier to achieve his dream of human/mutant equality. However, Legion traveled to a time when Magneto and Xavier were still friends, Xavier dies trying to protect Magneto, Legion vanishes, and a new time-line is created.
Magneto: Because of Xavier's sacrifice Magneto comes to believe in his late friend's dream of a peaceful coexistence between humans and mutants. Apocalypse chooses this moment as the perfect time to begin his world conquest. Magneto assembles this timeline's version of the X-Men just as Apocalypse begins his war.
Rogue: The Astonishing X-Men are led by Magneto's wife, Rogue. They were sent by Magneto to stop the cullings, which are being undertaken by Nemesis, Apocalypse's son and one of his horsemen. Nemesis manages to escape, however, and the team returns to Xavier's mansion where Rogue learns that both her son and her husband have been captured.
Cyclops: Factor X consists of the Elite Mutant Force (EMF), who serve Apocalypse. They are split into four sibling pairs, one of which is Cyclops and Havok. The EMF is tasked with maintaining control of Apocalypse's breeding pens, where people are imprisoned and experimented on. Havok later discovers that Cyclops is a traitor who has been helping people escape the pens.
Sunfire: Sunspot was a member of Gambit's team of X-Ternals, a group of mutants that stole from the rich to give to those in most need of help. Unfortunately, Magneto saw a much greater purpose for Sunspot and the rest of the team. He asked them to retrieve a shard of the M'Krann Crystal located in the Shi'ar Galaxy.