The first signs of the Age of X appeared in X-Men: Legacy #244; the events were removed from the Earth-616 mainstream continuity, with no memories of the alternate lives.

Using Madison Jeffries's absorbed powers, Legacy infiltrates the X-Brig (Fortress X's detention facility) to question Shadowcat.

[9] As she speaks with Shadowcat and touches a comatose Xavier, Legacy begins a mental attack on every mutant inside the fortress; seen by Danger, she becomes a fugitive.

As Magneto returns to the brig to free Shadowcat and Professor X, X (the voice controlling Fortress X) sends the Cadre after him.

When Professor X is freed, he telepathically shows his pursuers and a reluctant Legion the truth about himself and the reality in which they think they are living.

The Age of X was created when Legion's mind reacted to Doctor Nemesis's attempt to restore it to sanity.

Moira confronted Legacy and Gambit, revealing that she is also X. Cornered by Xavier, X launches a last offensive on the fortress.

[13] The mutant resistance was formed by Magneto to protect the surviving mutants from Graydon Creed and his mutant-hunters:[10] Other X-Men characters appear in the storyline in marginal roles and as inhabitants of Fortress X, including Angel, Anole, Avalanche, Beak, Bling!, Chamber, Colossus, Dr. Cecilia Reyes, Domino, Forge, Gentle, Indra, Jubilee, Lady Mastermind, Loa, Martinique Jason, Northstar, Rockslide, Scalphunter, Surge, Toad, Trance, Vertigo and Warpath (here known as Berserker).

[7] X used the brig to imprison Professor X, who knew his true nature[13] and convinced the other mutants that telepathic powers cannot exist; if they did, they would be very dangerous.