The X-Men are having fun outside when the Phoenix force suddenly appears in the sky. Shortly after, they find Scott freefalling from the sky. Rogue and Storm break his fall and bring him safely to the ground. Scott tells the X-Men that the “Dark Phoenix has returned”. Xavier telepathically calls for the X-Men to gather.
After changing into their X-Men uniform, they gather in Xavier’s office. Cyclops confides in Xavier that he had suspected for awhile that Madelyne could be “some kind of reincarnation of Phoenix”. As his doubts constantly lingered, Scott finally mustered the strength to ask Madelyne “point-blank if she was Jean reborn”. And in return he was whacked with “an energy bolt” from the Dark Phoenix and ended up at the Institute.
Xavier however is puzzled as to why Phoenix would attack Scott when she loved him. Also, Xavier had “sensed Jean’s death, years ago...but not his miraculous rebirth”. Xavier is not convinced of this “reincarnation” and wants to “find her and learn her intentions” before they make a move.
Xavier starts up Cerebro and gets electrocuted. Nightcrawler teleports him to the infirmary. Sprite checks on Cerebro and finds out “the safety locks have been disengaged”. It would otherwise have protected Xavier. Furthermore, Cerebro had been set to harm Xavier by using his own powers against him.
Suddenly, Cyclops appears to be engulfed in flames. Dark Phoenix emerges from his psyche, shocking the X-Men. The X-Men are no match for Dark Phoenix and are easily taken out one by one. Then, Dark Phoenix is gone in a flash.
Storm regroups the team, getting Sprite to contact the Starjammers and Scott down to the infirmary. Cosair reports that the Starjammers are also under attack by Dark Phoenix. The transmission cuts off ominously. They try contacting the Avengers but the transmission cuts before Storm can explain the situation to Captain America. Outside, the Phoenix looms.
The Dark Phoenix causes citywide destruction as the X-Men watch helplessly and tend to their wounded. As Cyclops’ unconscious body lies in the infirmary, his psyche separates from his body. As he floats through the Institute, he sees his mother in the distance. He approaches her but she warns him not to come too close. Cyclops is not supposed to die yet. She urges him to “look within [him]self” to find the answers that “will lead [him] to [his] heart’s desire”. Cyclops finds himself falling.
Suddenly, he wakes up. All his wounds are gone, as if nothing happened. Cyclops thinks that the Dark Phoenix might be a trick. Xavier was “zapped to prevent him learning the truth”. And it took someone twelve hours to transport him from Alaska to New York when the real Phoenix could do it in an “instant”. Cyclops figures he has identified the culprit behind this elusive attack.
But Cyclops is attacked by the X-Men, who think he is possessed by Dark Phoenix. Cyclops leads the X-Men into the Danger Room and initiates a training session. Outnumbered, Cyclops hopes to work the odds in his favour until he can convince his team mates of the charade.
Mastermind is revealed to be behind the scheme. He has tricked Cyclops and the X-Men into thinking that Madelyne is the Dark Phoenix reborn, as an elaborate ruse for his revenge. Madelyne is disgusted to learn of Mastermind’s true nature.
Cyclops takes down the X-Men slowly. When he has Rogue captured, he takes her to Xavier and makes use of her powers have her absorb Xavier’s knowledge of the situation to help convince the rest of the X-Men that they have been set up.
When Dark Phoenix unleashes a blast at Cyclops, Wolverine picks up the faintest trace of a gunshot. Rogue, now with telepathic abilities, relays to Wolverine that she is not picking up a psychic reading from Dark Phoenix, “almost as if she doesn’t exist”. Together, the X-Men work to defeat Mastermind.
Cyclops finds Madelyne dressed up in Dark Phoenix garb but otherwise unharmed. With Cyclops’ personal demons laid to rest, he and Madelyne are married. Before the ceremony, Scott goes to pay his final respects to Jean at her grave.
Scott: “I know your body isn’t here, Jean, it’s scattered molecular dust on the moon. But I like to think your spirit rests here, near where you were born, in this land you loved. We had such dreams. We figured we’d live forever. I loved you, Jean. I love Madelyne. I’m glad she isn’t you. What we had was magic--I’ll treasure it always. Now, Madelyne and I have a chance to create our own magic, to make what is as unique and special as what was. I hope you understand. Goodbye, Jean. Farewell...my heart.”
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