The Watcher explains the events that transpired with the Phoenix in the Marvel Universe, from how she was born to how she sacrificed herself on the moon. Unfortunately, in his reality the Phoenix had not sacrificed herself. Instead the X-Men lost and had to surrender Phoenix to the Shi’ar Imperial Guard instead, as he explains. The Shi’ar are far too afraid to kill the Phoenix, for they do not know how her lifeforce is bound up with the reknitted energy matrix holding back the neutron galaxy within the M’kraan crystal. So they burn out all of the brain centres pertaining to her powers, leaving her in essence an ordinary human.
Upon being returned to the X-Men, Jean is mentally crushed and defeated. She and Scott leave, and three weeks later marry without inviting anyone. Angel has bought them a house in Martha’s Vineyard, much to Scott’s disapproval. Cyclops doesn’t like taking charity, but realizes it is for the best and he could stay as a pilot that way while Jean recuperates.
Scott awakes in the middle of the night to find Jean smoking, and in their living room watching television as it reports the death of Senator Robert Kelly at the hands of mutant terrorists. Scott wants Jean to sleep, but she refuses. She tells him about how she’d wake up screaming from the same nightmare, the memories of what the Dark Phoenix had done. The Shi’ar wanted it that way, they left those memories in Jean for her to repent for years to come. Scott is speechless as she reveals this. When she was a telepath he didn’t need words, she could feel him and know what it was he meant to say, but she is no longer a telepath.
Jean compares her situation to being an artist without sight or hands, and Scott just wants her to stop and hear him out. She grabs her head while she runs into the rain, tears flowing. Scott finds sleeping pills, although she does not want to sleep, realizing she is considering suicide. He urges her not to give up as they lock in a kiss, the rain falling on them while Jean confesses her love once more. They are unaware of an uninvited guest nearing their balcony.
Magneto floats above their balcony, interrupting the tender moment while Scott pushes Jean to the floor and pulls off his glasses, firing a blast of extreme force at the X-Men’s nemesis. Normally it would rip through solid steel, but with Magneto’s magnetic force field he withstands the blast and sends the two flying back into their beach house.
Scott realizes they are no match for him alone, as the bindings of the floorboards snap up and wrap around Scott; sending his glasses flying to disable him as well. Slowly Magneto starts crushing Scott, until Jean yells out for him to stop. Magneto claims it wasn’t his intention to kill him, and he wants ‘Phoenix’ to come with him. Jean agrees while Scott yells for her to stay.
Magneto has brought Jean to his HQ, and as he sits at a table in his quarters drinking a glass of wine, Jean enters still only wearing her underwear despite Magneto having supplied her with a more covering outfit. He calls her ‘Miss Grey’ as Jean corrects him with a ‘Mrs. Summers’. As he asks her where the clothes are, she comments how she isn’t his guest but she is prisoner and doesn’t need his hospitality. Magneto comments on how passionate and alive she is, no wonder Wolverine and Scott both fell for her. Jean looks at him surprised, since she never told anyone about Wolverine’s infatuation.
Magneto moves on to explain how he knows everything about the X-Men since their last encounter, and the wall removes to reveal eight television monitors, one with each X-Man on it. Wolverine, Banshee, Nightcrawler, Cyclops, Colossus, Storm, Sprite, and Marvel Girl. He then explains how Xavier allowed the Shi’ar to mutilate Jean, and violate her. No one had the right to strip her mutant powers from her, and he has a proposal for the distraught Mrs. Summers. She asks why he is telling her this, and Magnus brings her to a room with a chamber situated in the center: it can restore her powers! Jean calls it impossible, but Magneto dismisses the accusation by saying anything is possible. If Science did it, it can be undone.
The X-Men’s blackbird hurtles out of the Earth’s atmosphere and towards Asteroid X, thanks to recent modifications by Anthony Stark. Nightcrawler explains the booster modifications at Scott pilots, a sense of coldness about him. Each X-Men holds their own thoughts about the situation, Nightcrawler of Scott’s coldness, Storm about losing Jean, and Wolverine about wanting to kill Magneto. Sprite is missing on this mission. As they near Avalon, they attract an asteroid to them to disguise them as they are pulled in towards the station.
Magneto plans for Phoenix to be reborn within the chamber and for her to work alongside him with his own goals and dreams. Second thoughts come to mind, considering that was what Mastermind had aimed for and had failed with miserably.
Jean doubts his intentions, calling him an enemy and not wanting to help her. Magneto dismisses it once more and tells her that no mutant should ever be stripped of their powers. He tells Jean how she has nothing to lose, which she repeats while her hand enters the chamber…
The X-Men reach the station and make their way in, Colossus thinking to himself how he is glad Sprite did not join them on this particular mission. When he gets back to Earth, he plans on telling her how he feels. The five X-Men make their way in looking for Magneto, whom they soon stumble across with Jean left in the chamber room to decide her own fate. All five of the X-Men gang up on Magneto, but he is able to hold them back for a short while.
Jean slowly begins to enter the chamber, the Phoenix Force flaring within, beckoning to her. Jean begins to feel it all coming back to her, being able to feel the universe. The sun, the stars, the galaxies, the life of everything suddenly rushing into her as she wants to walk into the chamber even more; but something pulls her back. Jean sees how she could save many with this power, but then thinks to herself: Jean to Phoenix, Phoenix to Dark Phoenix. The cycle is inevitable, how long could she really go without being turned back into someone who knows no love, but only hate, destruction, power, and death? Quickly Jean refuses and leaves the chamber. Picking up a rod she begins to destroy everything in the room.
Outside the X-Men have beat Magneto to a pulp, as Wolverine suggests ripping him to shreds. Magnus threatens to rip the adamantium from his bones as he feels Jean destroy his machine. Releasing a blast of electromagnetism, he throws the X-Men back and rips open the wall to the room stopping Jean and about to kill her. He stops as Jean tries to reason with him, telling him that the Phoenix would destroy them all once more. Mutants are only hated and feared because of men like him! Tired, he tells her that his future was decided long ago and wants them to leave.
The Watcher narrates the next few months. He explains how Jean had won the most important victory of her life, denying the power that would kill millions. She emerged emotionally whole once more, and still human. Jean and Scott can be happy together with her past behind her as Jean goes on to college to get her degree in education. Scott spends his time as a part-time X-Man as Rogue joins their ranks as well. Jean gives birth to a baby, whom she names Rachel. Soon after Jean becomesa teacher to the New Mutants, explaining to them many of her past experiences making her one of their best teachers yet.
Baby Rachel wakes up crying as Jean hurries to the crib, commenting on how quiet the large house has become. Xavier had mentioned that Rachel has telepathy, just like her mother once did which may be connected to her crying fit. Jean doesn’t want that life for Rachel, and wishes for Scott to be there. All of a sudden Scott walks through the door. Jean becomes ecstatic wondering where he and the X-Men have been. The two kiss as he suddenly reveals himself to be Jason Wyngarde, alias Mastermind. She screams as she backs away from him. He then creates the handsome illusion of himself, which he once used to seduce Phoenix to the dark side.
She claims to have never loved him, and he says how easy it was for her to escape responsibility and give into her deepest blackest heart’s desire. He explains how it felt being one with the universe, and thanks her. He was tormented forever by the memory of what he could never be again. So, he claims, he will return the favor.
Jean calls him the master of illusion, nothing more, with baby Rachel in her arms, crying. He says that the mind knows that his illusions are not real, but her senses are nevertheless overwhelmed by them. He makes her live through illusions of her bones breaking, her flesh burning, maggots eating her alive while Rachel becomes sprawled across the floor in tears. Her torment will be painful as well as everlasting, he claims. The X-Men will join her, including Rachel in the illusionary torment until he kills them one by one. She lies on the floor in fetal position, crying. All of a sudden, Jean snaps and elbows him in the face sending him on his back to where she pounds her fist into his head. She exclaims how him threatening her family gave her the will to overcome the illusion.
All of a sudden, Jean is whisked to the astral plane.
The puppeteer behind Jason’s strings reveals himself to be Amahl Farouk, the Shadow King. He drags Jean to the Astral Plane he explains how he was the first mutant Xavier ever fought, and killed his earthly body but he is immortal. He explains how he bided his time and took over the body of Mastermind as his new host, using him to get close to Jean. Jean says how she put her past ghosts behind her, as the Shadow King threatens to grind her soul to dust with a single thought. Amahl heads to kill Jean, while explaining that Rachel, heir to her power, will be his new host body;. Mastermind kills Jean with six bullet in the chest.
The Phoenix returns to Jean in her hour of need, as she lies there dying with Rachel gone. She doesn’t want it, but is forced to accept it as it enters her. In truth though, the Phoenix isn’t taking her. It is her! Jean awakens from the floor as the Phoenix, flames about her while she blasts out of the roof of the mansion, knowing that everything she believed in has been a lie.
Phoenix heads to Jamaica Bay, knowing the truth is here. Diving below the waters with a telekinetic shield keeping her alive, she heads to the bottom to find a cocoon holding the true Jean Grey in suspended animation. She is just the Phoenix force who had copied Jean. Realizing that she could never be Jean Grey, she needs to return what she stole. Her life is over as her spirits collapse, knowing it’s the end. Phoenix wishes Jean not to be there; for Scott could not accept her if it was true. Phoenix’s psycho-kinesis power instantly helps bring whatever she wishes to life and Jean disappears instantly. Phoenix stands there underwater, thinking there was no way she could have just done that…
The Watcher comments on the events which just transpired. He explains how he saw her save the universe and refuse her powers. He saw her destroy a world in an insane rampage, but he had never seen her take an innocent life.