Following the Dark Phoenix destroying the D'Bari system, Empress Lilandra of the Shi'ar meets with a galactic council on the threat that the Phoenix poses to the universe. The decision is unanimous in light of the evidence: the Phoenix must be destroyed. While on Earth, the Phoenix's presence does not go unnoticed, and receiving a warning from Dr. Peter Corbeau, the President of the Untied States attempts to contact the Avengers to find that only their butler Edwin Jarvis is present. When Jarvis terminates the call with the President, he notes that it was the Beast's turn to stay behind on monitor duty and wonders where he could have went.
The Beast is with his old comrades the X-Men, preparing for the Dark Phoenix's return by building a synaptic scrambler device to prevent Jean from using her powers. As Cyclops struggles to come to terms with what's become of Jean, Storm tries to console him. While down below in the Danger Room, Wolverine, Nightcrawler and Colossus attempt to blow off some steam in the Danger Room. They all come to agree that they must destroy Jean if they must, however their foremost duty will be to try and save her.

The Dark Phoenix meanwhile returns to her parents home at Annadale-On-Hudson and wakes up her parents and younger sister Sarah. Finding their thoughts impossible to keep out of her head, Jean attempts to keep her anger in check. However, she cannot and shows her family her powers by changing a houseplant into crystal. Noticing a fog outside Dark Phoenix realizes that the X-Men have found her and rushes out to meet them. Nightcrawler teleports behind her and places the synaptic scrambler on her head. Although this causes her great pain and limits her abilities, she is still able to hold her own against the X-Men's combined assault on her. When Wolverine gets close enough to her, she begs him to kill her with is claws, but Wolverine falters long enough for Phoenix's dark side to reassert control and blast him away. Having overheated the scrambler, Dark Phoenix removes it and locks the X-Men in stasis.
She begins to torture them mentally until she is confronted by Cyclops who tries to convince her to stop fighting and almost has her won over when Professor X arrives and attacks her mentally. This causes her to flip back to her evil persona and attack Charles directly. The two lock in mental combat and after a match of wits, Charles Xavier manages to use his mental powers to force the Dark Phoenix persona deep into Jean's mind restoring their sanity. Although the X-Men have a heartfelt moment now that Jean is back they all wonder how long her sanity will last. When John Grey and his family approaches Xavier to demand answers, they are shocked when the X-Men are all suddenly teleported away.

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