It’s a beautiful day and outside Xavier’s school Colossus and Wolverine cut away a dying tree, while Nightcrawler, Storm and Rogue watch and Kitty Pryde is more or less in the way. Rogue asks why Storm is so sad. The tree was pretty much dead from disease, anyway. Storm explains that she once believed herself to be a caretaker of all living things. She should have sensed the tree’s illness. Why such a big production, Rogue wonders. She or Colossus could have easily pulverized the tree. More fun this way, Storm explains, plus it’s an opportunity to exercise both powers and teamwork. Rogue is just about to joke that Storm’s sounding just like the professor, when they are blinded by a flash. A huge burning firebird appears in the sky and is gone as quickly as it appeared. However, in its stead is a man falling. Rogue and Storm take to the air and catch the man – their teammate, Cyclops. Storm asks Nightcrawler to take Scott to the infirmary. There’s no time, Scott interrupts her. Haven’t they seen? Dark Phoenix has returned!
Xavier mentally addresses the X-Men and tells them to join him in his study, which they do after donning their uniforms. Cyclops quickly briefs them: first, there were his fears about Madelyne Pryor being the reincarnation of Phoenix, doubts he couldn’t put aside. Last night, in Alaska, he asked her if she was Jean reborn and got darn near incinerated by an energy bolt as a result. The last thing he remembers before Rogue caught him is Dark Phoenix standing over him laughing.
Xavier wonders: some things don’t add up. Jean lovedCyclops. Why would she hurt him? And why would she then heal those fatal injuries? Their first step must be to find her and learn about her intentions. Storm asks whether they shouldn’t summon reinforcements. Phoenix is a cosmic entity, after all. When he’s convinced of the threat, Xavier replies, donning the Cerebro helmet. He sensed Jean’s death years ago, but not this miraculous rebirth and he should have. He switches Cerebro on, but the moment the system is activated, it sends a jolt of electricity into him. Rogue swiftly reacts, cutting the power. Nightcrawler takes the unconscious Xavier into his arms and teleports him to the infirmary, hoping that the strain of teleporting won’t worsen Xavier’s condition.
Wolverine wonders. Cerebro is supposed to have automatic safety systems to prevent that kind of massive feedback. That zap was awfully convenient. Kitty checks Cerebro and finds Wolverine’s suspicions confirmed: the safety interlocks were disengaged, meaning the Professor’s amplified powers were reflected back at him instead of outwards But how can that be? Storm wonders. They saw every move he made – the settings were correct… but now they are not. Actually, there’s a simple explanation Cyclops pipes up. What is it? Storm asks, turning to him, only to shout his name in horror, as Scott starts to smile evilly and burn. As flames rise from him, he states, “would you believe, the end of the world?” The flames solidify into Dark Phoenix, stating “hi guys! Miss me?” while Scott collapses.
Storm attacks her former friend with bolts of lightning. Dark Phoenix mocks her effort. What makes Storm think her lightning will be more successful this time than it was last? With those words, she reflects it back at Storm. Colossus shouts at her to stop. She’s killing Ororo! Not yet, Phoenix replies, she wants to play a bit first. Closing her fist, she makes Colossus telekinetically feel immense pain. This has, of course, Kitty and Lockheed react. Kitty figures that Phoenix is comprised of energy. Perhaps phasing through her, she can short circuit Phoenix. Instead, Phoenix reflects the pain back at the girl and swaps Lockheed away.
Rogue rushes at her, but Phoenix easily grabs her by the collar and tosses her away. Jean sure hasn’t lost her touch, Wolverine who hasn’t moved states. Phoenix mockingly thanks him and comments that he has unsheathed his claws. Does he care to try his luck? Nope, he replies. Smart move, she agrees. She has some errands to run, but when she returns they can pick up where she left off. With those words, she disappears, surrounded by the Phoenix effect.
Storm tells Colossus to help her bring Scott to the infirmary. Kitty is to contact the Starjammers and Wolverine should go find Rogue.
Minutes later, surrounded by the others, Kitty keeps on trying to reach the Starjammers, but there’s massive interference all across the spectrum. Event their laser and subspace com-links are being scrambled. Phoenix’s doing, they all agree. Kitty finally gets through, only to see are very beaten up Corsair, telling them that Phoenix attacked the Starjammer, the others are dead and now she’s coming to finish off the ship. He asks them to tell his sons he loves them and before the horrified X-Men’s eyes Corsair dies.
Kitty contacts Avengers Mansion next. Captain America appears on the screen. Storm starts to brief him on the situation, but suddenly the ground shakes and Cap screams in pain. The transmission breaks off and the X-Men see the Phoenix effect rising outside over what s left of New York City.
Soon, in the infirmary, while Nightcrawler busies himself with treating the unconscious Cyclops, Storm tells him the grim news: Kitty patched into a military satellite for an aerial view of New York: there’s nothing left but a cauldron of molten rocks. Everybody who might have helped them is dead.
Nightcrawler announces that he has stabilized the Professor but Scott is a problem. Physically, he is in perfect health, shouldn’t even be unconscious. Yet, his condition deteriorates as if Phoenix had stripped him of his will to live. There is nothing he can do but pray. The two X-Men head for the door, letting the autodocs care for the patients, unaware that a part of Scott is very aware of what is going on – or so he thinks. His astral body floats over his real body, which he perceives as blistered and charred from Phoenix’s energy bolts. Strangely, he doesn’t mind. His real self is up there, unhurt. He sees Ororo looking sad, trying not to let it show, the way he used to and wishes he could comfort her, but he can’t. She’s alive. He is not.
As the others leave, the room is flooded by a white radiance that draws him closer. He realizes he is dying and a part of him wants to fight, but mostly he wants to embrace the light. Around him, he sees phantoms of people who have gone before, but he is looking for one in particular. He can feel her through the psychic rapport they once shared. He sees a woman, clad in white, stepping out of the light, but it is not who he thought. The ethereal blonde tells him to stop. Calling him her “darling-boy,” she tells him the place is not yet for him. He asks who she is as they drift apart. She tells him to look into himself. There, he’ll find the answers and they will lead him to his heart’s desire. Over his protests, he tumbles into darkness, hearing her whispered farewell. To late he recognizes her and shouts “mom!”
Miraculously, Scott awakes and cries, as he remembers who he was looking for and how certain he was that he’d find her. Somehow, he never really accepted what happened, but now he has no choice. Jean Grey is dead. But then who is their foe? Last night, Madelyne transformed into Dark Phoenix and blasted him, then healed him. Today, he got blasted again, but now there is no scratch on his body. What if he only thought he was burned, he wonders as he gets up. What if there’s no Phoenix either and this is all a trick? It would explain why Charles was zapped before he could learn the truth. Or why so much time passed between Phoenix’s manifestations. Why the twelve hour delay – unless someone had to use a plane to fly from Anchorage to New York. Who has that kind of knowledge and hatred? Who can play with reality and is obsessed with Dark Phoenix? Only one person fits the bill, Scott realizes. He has to warn the others and flush their foe out. He must use the advantage of surprise, since he is believed to be dying. Scott fervently prays that the villain has done nothing to Madelyne, as he makes some preparations and, ten minutes later, he runs to join the other X-Men, a little portable control module at his side.
His teammates are less than pleased, though, calling him “murderess.” Storm yanks him inside with a gust of wind and Cyclops realizes that their foe is making them see him as Dark Phoenix. Cyclops urges the others to listen. Nothing they see or hear is real. Why should they believe her then, Colossus replies and punches him, cracking some of Cyclops’ ribs. Scott retaliates with a high power optic blast into the Russian’s face, realizing the X-Men are not pulling their punches. Knowing the team intimately, he uses their own tactics against them.
First, he tricks Nightcrawler into teleporting away- enabling him to nail Wolverine who stood behind the teleporter and then he maneuvers Colossus’ body to topple Storm and Rogue. Quickly, he shoots his blasts upwards, knowing that Nightcrawler likes to reappear above foes and tackle them from that position. Paydirt. Next, he is attacked by the fire-breathing, little dragon, Lockheed. Having no idea what kind of punishment Lockheed can take, Scott chooses to make his exit, but finds himself tackled by Kitty, who phases through the wall and grabs him. Cyclops throws them both off the balcony, leaving Kitty no choice but to phase both of them down and into the Danger Room.
The other X-Men realize where they’ll end up. Storm orders Nightcrawler to teleport to the Danger Room’s control booth and arrange a proper welcome for Phoenix. She also asks him to spare Kitty, if he can, but against this foe their lives are expendable. Cyclops sees as a flash of light in the control booth, as he and Kitty fall into the room, and realize it’s Nightcrawler. Cyclops kayos Kitty with a nerve-pinch as she instinctively solidified. He then uses the portable module he prepared before he alarmed the X-Men to create an airbag to cushion their fall and then to electrocute Nightcrawler before he can disengage the safety protocols. As the others race into the room, Cyclops uses the module again to create a facsimile of the Savage Land. He’s standing on a cliff, while Colossus and Wolverine fall, leaving Storm and Rogue no choice but to dive after them and save them.
Rogue wonders where they are and Storm explains the Danger Room’s illusions to her. Wolverine correctly points out that “Jeanie” is capable of creating her private realities. Why bother using Xavier’s gadgets? Isn’t she that powerful after all? Is she toying with them? Storm orders Wolverine to follow Phoenix’s trail. Hiding in the foliage, Cyclops can hear from Ororo’s tone of voice that she’s made her decision to kill Dark Phoenix. Five to one odds, he thinks, but on the other hand he controls the room, which will not only throw off the X-Men but their true foe as well.
Elsewhere, in what appears to be hell, with lava-pits and fire, said true foe applauds Cyclops for his ploy: confront a master illusionist with his own illusions. Opposite Mastermind stands a very confused Madelyne Pryor dressed in the Dark Phoenix costume. Is she crazy, she wonders. Is she dead? Is this hell? Mastermind mocks her with elusive replies, until he finally introduces himself as Jason Wyngarde AKA Mastermind. A villain who, with Madelyne’s help, will destroy the X-Men.
Mastermind reaches for her and Madelyne is amazed as “hell” turns into an ordinary room. As far as he is concerned, Mastermind brags, reality is what he chooses to make of it and they are all just pawns. Wyngarde tells Madelyne of his revenge plan: he has convinced the X-Men that Dark Phoenix has resurrected herself and has embarked on a murderous rampage. He will further convince them, as he has Cyclops, that Madelyne is Phoenix. To save the universe, they will kill her – an innocent and Cyclops’ love. From that blow, they will never recover.
Angrily, Madelyne strikes him to find that he was only an illusion. Another Wnygarde appears behind, her asking how she can stop him? For all she knows he isn’t even in he room, if there is a room at all. Perhaps she has gone insane, after the 378 passengers entrusted to her care died at her hands…Madelyne angrily protests that this was an accident. Why is he doing this to her? Because, when he looks at her face, he sees Jean Grey and his own damnation. Phoenix made him one with the cosmos. He touched the power of God, but the experience drove him insane. He recovered but cursed with the knowledge of what he’d been and could never be again. Thanks to Phoenix, his life is an unending torment. And if he cannot avenge himself on her, he’ll let her beloved X-Men suffer in her stead.
Explaining how he stalked the X-Men for months – as well as settling scores with some old colleagues – Mastermind shifts from Japanese crimelord Nabatone to the priest Scott met on the plane to Cyclops himself. He tells Maddie that he had planned to use whoever was Scott’s girlfriend at the time. Madelyne’s uncanny resemblance to Jean provided a delightful and unexpected irony, making it all the easier to convince Scott. Madelyne, not quite getting it, believes that it is truly Scott standing in front of her. He kisses her passionately and then, suddenly, changes back to his scrawny, ugly true form. Madelyne turns away in disgust, while Mastermind, changing back to the handsome Wyngarde persona, mockingly tells her that he could make her love him, whatever his appearance. And may yet do so.
In the Danger Room, which Scott has changed into a jungle scenario, Cyclops runs, planning ahead. The jungle is to keep Rogue and Storm from attacking him from the air. Scott climbs up a tree and waits until Wolverine and Colossus have passed him. Scott attacks Wolverine with an optic blast from above, then runs and climbs trying to stay a step ahead of the angry Colossus. The trick, he thinks, is to keep the X-Men off his back, but yet leave them able to fight for the eventual confrontation with Mastermind. Cyclops manages to trap Colossus in some quicksand. The jungles ends and mountains appear ahead. Taking out a breathing mask, Scott starts to run towards the cave – the Danger Room’s exit – figuring that Storm will strike first with her lightning.
Storm wonders why Phoenix bothers running. Is this a game? Or is there another explanation? She strikes with lightning but hesitates somewhat, throwing the bolt off-target. Cyclops reciprocates with an optic blast. Rogue catches her and lands opposite Scott in a field of Oz-poppies, which Scott activates with a wide angle shot. Rogue faints as the dust was specifically keyed to affect her physiology. Scott had prepared this when he pulled her medical file to program the Danger Room. He carries the unconscious girl and as he leaves, he programs the computer to shut down the entire house, including the surveillance systems, which Mastermind must have used to watch the show. He won’t know where Cyclops is and will have to come after him personally.
Cyclops heads for the infirmary, where the still unconscious Xavier lies. He puts Rogue down on a chair next to Xavier, awakes her with some smelling salt and then puts her naked hand on the Professor’s forehead, forcing her to absorb his telepathy. Rogue is drowning in her new powers but Cyclops insistently shows her how to rein it in and control it, thanks to everything taught to him by Xavier and learned through the rapport with Phoenix. Eventually, Rogue calms down, just as the rest of the team gathers.
Cyclops once more implores them to listen, that they are being tricked. Why is he bothering to talk to them if he is Phoenix? On Cyclops’ order, Rogue creates a mindlink with the others and they finally see the truth. Still suspicious, Wolverine asks how they’ll know this isn’t a trick. “Because, little man” a voice announces, “the trickster is right behind you.” It’s Dark Phoenix all powered up, but Scott doesn’t buy it and shouts that Mastermind’s Phoenix no longer fools them. She’s a fake and can only harm them if they let it. Phoenix fires a blast at Scott, a blast that, Wolverine realizes, conceals an actual gunshot. Rogue telepathically informs Wolverine that her psi-probes don’t register anything from Phoenix, as if she doesn’t exist. Wolverine agrees, telling the others that there is a dead zone in the room, that his senses can’t focus on and he felt the same when Xavier got zapped. He tells Storm that Cyke was right and Mastermind is in the room. They have to ensure he remain, Storm relpies and whips up a horrifying tempest out of thin air that even her friends cannot withstand.
Rogue tries to shield Xavier with her body, Colossus orders Kitty out and Kitty wonders if Ororo is under Mastermind’s control. Deciding it is enough, Storm quickly disperses the Storm again, musing that once this display would have left her exhausted, but violent weather comes easy to her now. The infirmary’s door opens, letting the flood out and a half-drowned Mastermind lies in the corner. Wolverine heads towards him with unsheathed claws clearly intending to kill him, only to be stopped by Storm. It’s one thing to kill someone in the heat of battle, but not a helpless foe. She orders him to find some drugs to keep Mastermind unconscious, while the others take care of their wounded.
With the remnants of Xavier’s psi-powers, Rogue realizes that Storm was not only willing to kill Mastemind, but to sacrifice the X-Men in the process. Kitty returns with an emergency medical kit, while Scott drags himself up, despite his injury to look for Madelyne. He finds her lying facedown in the water and hurries to her side. Fears race through his head as he finds that she is unconscious and has no pulse. He’s afraid of history repeating itself, of helplessly watching the woman he loves die again. Administering CPR, he urges Maddie to drag herself back to life for him, as he did for her. Finally, she coughs and comes to, asking his name. The couple hugs.
Several days later, Scott, dressed in a tuxedo, stands at Jean Grey’s grave at St. Stephen’s Chapel. He addresses Jean, stating that he knows she doesn’t lie here – her body is scattered molecular dust on the Moon, but he likes to think that her spirit rests here near the place she was born and the people she loved. He reminisces about their love and, putting a bouquet of roses at her grave, tells her that he loved her. He loves Madelyne. He’s glad Madelyne isn’t Jean. What they had was magic, but now he and Maddie will have their own chance to create magic. He hopes she understands. With a last “Goodbye, Jean. Farewell… my heart” he leaves.
Later that afternoon, in a huge tent erected in front of Xavier’ school, X-Men, past and present, New Mutants, friends and relatives have gathered for the wedding of Scott Summers and Madelyne Pryor. With everyone getting ready, best-man Alex Summers teases his nervous brother a little. Scott’s grandparents comment on how handsome their grandsons are - especially Scott - and their son, Chris Summers, thinks melancholically that he only wishes his wife, Kate, had lived to see that day.
Corsair’s friends, the Starjammers, are watching from orbit and his lover, Hepzibah, comments, equally sad, that Chris is thinking of his first wife. Raza comforts her: fond memories don’t mean Chris loves her any less and Ch’od wonders if Scott is still interested in leaving with them.
Back at the celebration, Wolverine quips to Kitty that he hopes she’ll have more luck as a maid-of-honor this time. Knowing what pain the remark hides, Kitty wishes she could do something to put things right between Wolverine and Mariko again.
A gentle fanfare heralds the entrance of the bride, led in by an elderly man.
The ceremony starts and all the couples among the X-Men, Kurt and Amanda, Lilandra and Charles, Moira and Sean, even Kitty and Peter share meaningful looks or gestures. Only Wolverine looks away, bitterly, while his friend Carol Danvers clearly pities him.
With the ceremony over, Scott and Madelyne finally share their first kiss as husband and wife.