Suspecting Emma's hand in Jean's abduction, Wolverine places her in a holding cell. Emma is later freed by Cyclops, who trusts her to find Jean. Apparently, the Hellfire Club had become aware that the Phoenix Force had possessed Jean and supposedly wants to extract the divine Phoenix Force from her mind and use its infinite and limitless power and strength for their own ends. Meanwhile, Magneto hatches a plot against the human race, having replaced Senator Kelly with Mystique to start an attack on Genosha. In the future, the Professor is apprehended by Sentinels, who have replicated Cerebro to find all mutants in the world.

Emma discovers the Hellfire Club's true motivation for using the Phoenix Force, and fights to free Jean alongside Cyclops. In Genosha, Magneto's plan comes to fruition as Sentinels ravage the island, providing just cause for Magneto's war against humanity. Accordingly, Magneto reprograms the Sentinels to attack humans. In the future Professor X and the future X-Men are freed by Wolverine, and together they take up a fight against Master Mold.

The X-Men, MRD and S.H.I.E.L.D. fight against Magneto's Sentinels. Meanwhile, the Inner Circle reveals to Scott that Emma and the Stepford Cuckoos were the ones responsible for setting in motion the events that would lead to the destruction of the mansion, Xavier's twenty-year coma and the eventual extraction of the Phoenix Force from Jean's mind and body. Upon the successful transmission of the Phoenix Force from Jean and into the bodies of all five Stepford Cuckoos, the possessed girls are then instructed by Sebastian Shaw to destroy the Sentinels, the X-Men and Genosha, an action which was completely unknown to Emma whose initial plan was to both locate and destroy the cosmic entity before it could reach maturity and bring forth unparalleled global destruction. In the wake of her regretable actions, Emma attempts to redeem herself in the eyes of the X-Men, especially Scott, by ultimately sacrificing herself in order to successfully destroy the Phoenix Force entity. In the aftermath of the carnage, Magneto is banished from Genosha for his radical actions while his eldest daughter, Wanda, assumes authority over the destroyed island and its inhabitants, alongside her sister Lorna, in an attempt to rebuild from the demolished remains of her father's mistakes. From the future, Xavier informs the X-Men that their mission was a success and that the bleak, sentinel-run world has now been avoided. However, there is a new and far more formidable future that has taken its place: the Age of Apocalypse.