Warring Mutant Factions Destroy the Golden Gate Bridge - Late 2006
The events of "X-Men: The Last Stand" take place.
Jean Grey is resurrected as Phoenix. Cyclops is killed. Phoenix kills Xavier and joins Magneto. X-Men and Brotherhood of Mutants battle another until it culminates in Wolverine killing The Phoenix. Xavier transfers his consciousness into his twin brother's comatose body.
Worthington Labs introduces a vaccine that claims to eradicate the X-gene, leading to violent uprisings from mutant factions that resulted in the destruction of the Golden Gate Bridge. Recognizing the need to improve human-mutant relations, the President appoints Beast as ambassador to the UN.
Note: The explanation that is given for Charles's resurrection (and elaborated in the tie-in novel) is that Charles had a twin brother named P. Xavier. P. Xavier was born into a comatose state that he stayed in his whole life, theoretically because of Charles's psychic abilities in the womb being so powerful and uncontrolled. P. Xavier eventually ended up as a care subject of Moira's who Charles transfers his consciousness into when Jean kills him.
His paralysis in his new body could be due to atrophied spine muscles, or the explanation given in Days of Future Past, where his paralysis and telepathy seem to share a relationship.
(Explanation found in DVD Commentary for X-Men: The Last Stand during the credits.)