Planet earth is under attack by the Phalanx, a race of techno-organic aliens seeking to assimilate all life on earth. Warlock, Beast, Forge and Mr. Sinister, and Amelia Voght develop an anti-virus and a plan to administer it at the phalanx core. They recruit Magneto and he is able to obtain a phalanx sample. Hodge explains to them what the Phalanx is doing and how he came to be part of them. The group enters the Spire of the Phalanx and attempts to rescue the others and eliminate the phalanx with the anti-virus.

Cyclops, still in mourning after Phoenix's death, quits the X-Men and returns to the orphanage he grew up in and encounters his friend Sarah. Cyclops suspects foul play of Zebediah Killgrave, Sarah's wealthy benefactor as he begins to adopt mutant children for an unknown purpose.