The Imperial Center, ruling seat of the Shi’ar Empire, located halfway across the know universe from Earth. The situation is grim.
The assembled council members witness Dark Phoenix approaching her homeworld on a screen, as Maestrix Lilandra arrives to open the emergency meeting. Lilandra quickly apprises them of the situation. The empire – the entire universe – now faces a threat that may even make Galactus pale into insignificance in comparison. To feed his hunger, he devours worlds. Phoenix may well consume all that exists.
She orders one being, called Tuoks’enhaamin, to begin the briefing. He complies, explaining to everybody what they are seeing in front of them on a hologram: Upon arriving in Imperial space Phoenix plunged into the heart of D’Bari, a main sequence, G-type star. Within seconds, the star went supernova. The resulting stellar explosion destroyed not only the sun but its inhabited worlds as well. After leaving, Phoenix was intercepted by their newest, most powerful battle cruiser. The ship attacked and was destroyed as easily as the star.
Lilandra now speaks, telling the councilors of her first meeting with Phoenix. Back then, Jean Grey was a beneficent entity. She and her fellow X-Men helped prevent Lilandra’s brother from unleashing Armageddon. Now, she is beneficent no longer and may well pick up where D’ken left off. If the universe is to survive, Lilandra concludes on a somber note, Phoenix must be destroyed.
At that moment on Earth, in the White House, President Carter learns from Dr Corbeau that the energy matrix that Starcore had monitored earlier that evening is returning to Earth and it is far more powerful. The president calls the Avengers. At Avengers Mansion, the butler, Jarvis, notices the special alert, which only the president can activate and only in times of gravest danger. He activates the intercom and the disgruntled president asks why there wasn’t an Avenger on monitor duty as there is always suppose to be. He’d been calling for some time without answer. He then explains the situation and wants the Avengers ready to deal with this threat. Jarvis stutters that he will assemble the team at once. After the transmission ends, he wonders why Master Beast isn’t here anymore. He was on monitor duty. There is no message but where could he have gone?
The answer is to his old friends in need, the X-Men. At the X-mansion, Beast is busy assembling a mnemonic scrambler. Slip this on Jean’s head, he predicts, and she shouldn’t be able to think a coherent thought, much less read minds or throw telekinetic force bolts. Cyclops commends him on his work and Storm silently worries about Scott. Soon, they will have to fight the woman he loves – perhaps to the death. Storm reaches out, but Cyclops gently rebuffs her. He knows she is trying to comfort him, but he cannot give full rein to his feelings right now or he’ll shatter. For Jean’s and the others’ sake, he has to stay strong.
Meanwhile, in the Danger Room, the rest of the team is going through a workout. They quickly dispatch of their mechanical foe, only to find the workout doesn’t really make them feel better. Jean is special to all of them. They wish to save her, but are aware that she trashed them easily before…
The woman on everyone’s mind is returning home, not to the X-mansion, though, but to her parents’ home in Annandale-on-Hudson, a little college hamlet some fifty miles northwest of the X-Mansion.
Dark Phoenix silently enters her parents’ home, taking in all the familiar sights, yet her memories now seem to belong to someone else. Suddenly, lights go on as John Grey comes downstairs, asking who’s there. ‘Would you believe the wicked witch of the west,’ his daughter jokes. John is happy to see her and calls for his wife and Jean’s older sister, Sarah, to come down.
Jean first rushes to embrace her father, but then becomes horribly aware of the fact that her telepathy has grown so sensitive she cannot block out his thoughts anymore. He’s an open book. Nothing is secret or sacred anymore. It is the same with Sarah and Elaine, who both seem happy to see Jean. Nevertheless, Jean can perceive thoughts and feelings they may not even be aware of. Her parents are worried about her but, buried beneath that, on a primal level, she scares them. Jean brushes her mother’s questions off, reacting more and more to the feelings she cannot shut out. She feels Sarah’s primal fear that her two children will be mutants like Jean. And what’s wrong with that? Phoenix decides angrily. After all, she holds the fate of the universe in her hands.
No longer able to help herself, she tells them that they have good reason to fear her. She transforms potted plant into crystal to make her point and threatens that she could do the same to them. Fear tuning to anger, John angrily asks what she is and what she wants from them. Jean cryptically replies that she is what she is and that she once was his daughter. Even while she is hurt by his outburst, Phoenix threatens him.
Suddenly, she notices the fog outside that sprang out of nowhere. She flies outside, realizing that Storm is probably behind that phenomenon. Nevertheless, she cannot spot her or the other X-Men telepathically. Suddenly, Nightcrawler teleports onto her back and fastens the scrambler headband around her brow. She manages to shake him off and screams in pain a second later, as the scrambler goes active. She can barely concentrate but, nevertheless, refuses to give up. The diadem cripples her power but she is still not helpless, as Colossus has to learn when he tries to grab her-
Storm realizes that, evil though Phoenix is, she is still Jean with all her strength and courage. She will not yield. Ororo tries to appeal to Phoenix, who coldly informs her that, while Ororo may be closer to her than her sister, she still won’t hesitate to strike her down and proceeds to do so.
Beast grabs Phoenix next and holds her in place, while worrying that the Phoenix will soon burn out the scrambler. Wolverine jumps at Jean, intending to finish this the only way, he feels, it can be finished, over Beast’s protests. He asks Jean to forgive him as he unsheathes his claws. Tears in her eyes, Jean asks him to do it, to strike while her human part is still in control. Wolverine hesitates for a moment, as the real Jean’s back. The moment passes and Dark Phoenix reasserts herself, telekinetically pushing him away. She tears off the burnt-out scrambler from her brow, gloating that this was an admirable ploy but now it’s finished.
With a gesture, she telekinetically freezes all X-Men and tauntingly asks what she shall do with them. Colossus tries to appeal to her humanity. She assures them that there isn’t any left and asks if he has any last thoughts before final sentence is passed.
Suddenly, Cyclops appears, asking her to stop it. She tells him she was wondering when he would show up. With an evil grin, she adds that she hopes he has come to fight. He came to talk, he replies calmly. She won’t listen, she shoots back. Then she should kill him, he suggests. After all, he cannot stop her. He won’t even try. He urges her to be true to her malefic destiny. If she can. But, he continues, if she cannot, she should ask herself why. She is Dark Phoenix, power incarnate. Nothing can stand against her. Yet the X-Men have defied her and still live. Why?
After some hesitation Phoenix, replies that they aren’t worth killing. Scott calmly insists that there is another answer. She is Dark Phoenix. But she is still Jean Grey. She cannot exorcise that fundamental part of herself. She can’t kill them, because she loves them.
Neither of them notices that an aircraft is closing in, as Dark Phoenix protests almost defensively that she knows nothing of love. Scott comes closer, as he reminds her of all she has done in the name of love. How she died for them, resurrected herself for him, how she almost died again saving the universe. She islove. Can she deny that? Deny herself?
He has reached her and Phoenix is torn. A part of her wants to deny it, another part appeals to Scott telling him that she hungers for a rapture beyond comprehension. That need is a part of her too and it consumes her. It doesn’t have to, Scott assure her, almost touching her.
At that moment, a psibolt hits Phoenix from the back. Xavier has arrived on the scene. Scott shouts at him, while Xavier assures him there was no alternative. Quickly recovering, Phoenix telekinetically tosses Cyclops aside to turn to Xavier, angrily shouting that he has just signed his death warrant. Xavier grimly assures her that he is part responsible for what has happened to her and, though it may cost him her life, he will set it right.
Summoning her power, Phoenix mocks that he almost sounds guilty. As well he should. He unleashed her telepathic power. He set in motion a chain of events that created Phoenix and Dark Phoenix. Now pinkish red, an energy raptor rises around Jean as the telepathic battle between them begins, waged on several planes of existence. The raptor eventually wavers and fades, as Xavier manages to bind Dark Phoenix within an unbreakable network of psionic circuit breakers. As Phoenix collapses, Jean Grey once more, Xavier is aware that he only won because Jean was fighting her Phoenix self and helped him succeed.
Scott runs to Jean’s side, shouting her name. For a moment, he fears she’s dead. What, he wonders, if she is still Dark Phoenix. He’ll love her just the same, he decides. Jean, coming to, smiles and tells him those thoughts sounded a lot like a proposal. They did, Cyclops agrees. So what does she say? She says ‘yes,’ as they kiss. The X-Men and the Greys have, in the meantime, joined the scene. Just as Xavier is about to explain to a disgruntled John Grey what has been happening, there is a flash of energy and the X-Men are gone leaving the Greys with the fear that they may never see Jean again.