The Xavier Institute for Higher Learning, Westchester, New York. Emma Frost a.k.a. the White Queen sits in Cerebra and calls out to Scott - to anybody - but gets no reply. Telepathically, Emma calls to Jean, asking her if she is responsible for this. Emma admits that she stole Jean’s husband, but tells Jean that he is happier now, and points out that Jean is practically infinite now, a part of the whole universe. Emma asks Jean if she can forgive her, ‘can’t you just look into my soul and see the…see the love in there? Jean? God, I sound like an idiot!’
Meanwhile, Ororo “Storm” Munroe and Kurt “Nightcrawler” Wagner hover high in the air - right in front of a Shi’ar spaceship. Using the computer on his flight-cycle, Kurt informs Storm that there is no communication from the mansion - conventional or telepathic. Storm declares that Dark Phoenix has returned at that everything is wrong. Kurt asks if they should go home, and Storm agrees - but only after the deal with the Shi’ar spaceship.
Storm introduces herself to the ship’s crew and points out that they are flying an armed Shi’ar Destroyer, unannounced and under cover within Earth’s atmosphere, and asks them to explain their presence. The ships commanding officer tells Storm to get out of the way or die. Storm tells Kurt to teleport them inside, but as Kurt begins to do so, the helmsman is ordered to move the ship - and Kurt misses his target.
Nightcrawler is disappointed he missed, but Storm tells him it is not his fault. Kurt asks what Storm thinks it is the Shi’ar want, to which Ororo points out that if they were here to exterminate all mutants again then they would have already attacked. Therefore, she assumes that the Shi’ar know Dark Phoenix has returned and that they have come for Jean.
Storm tells Nightcrawler that they have to follow the Shi’ar, who are now flying away. ‘You mean we have to stop them’ says Kurt - but Storm has a different opinion and tells Kurt that he may be right, or perhaps they will have to help the Shi’ar. ‘Are you ready for that? Think about it, and hold tight’ With that, Kurt holds onto Storm as she flies after the Shi’ar.
Back at the Xavier Institute, Emma telepathically declares that this is so passive-aggressive it is actually embarrassing, and asks Jean if she wants to fight, then why doesn’t she? Emma admits that Jean would atomize her within nanoseconds, so she doesn’t know why she is suggesting this, except that maybe she is going a little insane being frozen in the dark with no idea when or if she will ever see or hear another persons face or thought ever again - suddenly, she screams, as she hears someone in her head!
It’s Scott “Cyclops” Summers, her lover and co-headmaster of the Institute - not to mention Jean Grey’s former husband. Emma asks Scott if he is all right, and using their psychic link, Scott replies that he is fine, and tells Emma to stay in Cerebra, as he needs her there. Emma asks where Jean is, and Scott informs her that Jean wasn’t responsible for freezing everyone, that it was Quentin Quire, who had reconstituted himself, smashed his tank and telepathically froze everyone.
After Cyclops asks Emma if she can find him, Emma replies ‘Quentin…that little runt’ and informs Scott that his energy is off the charts and heading North, incredibly fast. Emma suggests that this isn’t coincidence and reminds Scott that Quentin is an Omega-level mutant, just like Jean.
In the Beast’s lab, Scott tells his friend, Dr. Henry McCoy to get the egg into the jet along with any equipment he will need to finish it. Emma suggests that Jean must have brought Quentin back for some reason, when suddenly she screams, announcing that Archangel is screaming in her head and that there is a message from Logan. ‘We found her!’ announces former X-Man Warren Worthington the Third, a.k.a. Archangel and close friend of Jean Grey.
Cyclops, Emma, Archangel, Kitty “Shadowcat” Pryde and the Beast take their sears in one of the X-jets, Beast securing the egg as Piotr “Colossus” Rasputin enters the aircraft and declares that he is coming too. But Cyclops tells Peter that he isn’t, and informs him that he is to stay and watch over the children. Colossus protests, reminding everyone that Jean was his friend - but Scott barks that he gave an order, and tells him to close the hatch. As the hatch closes, Colossus looks inside to Kitty, who whispers that it will be all right - and as the jet takes off, she phases her hand out of the craft to touch his, before Colossus can only watch as they leave for a painful mission.
Inside the jet, Warren tells Scott that they could have used Colossus, to which Scott replies that he knows, and would want him at his side in any other fight, but reminds everyone that Colossus had a chance to kill Dark Phoenix last time around - and he pulled his punch. Warren points out that Piotr wasn’t the only one, but Scott just declares that they cannot make those kinds of mistakes again, or all of them - every living creature on this planet could pay the price.
Cyclops tells everyone that he knows they are all thinking that maybe it's really Jean and maybe they can reach her and save her. ‘And maybe your fearless leader keeps insisting it’s Dark Phoenix because he’d rather fight a monster than face his own wife’. Everyone listens intently as Cyclops admits that he will probably feel guilty about the way he handled his marriage with Jean until the day he dies, but that it doesn’t affect the fact that he knows Jean Grey, fundamentally and forever, and that he will always honor her in life and death.
He states that means he will never forget that first and foremost Jean was a hero, and right now id she is really inside the Phoenix she is fighting it like a champion, just like Logan said, and that is why they are the right people for this job. Scott knows that all of them combined could never beat the Phoenix in a straight fight, but Jean knows them, and trusts them - so she is going to give them every opportunity to do what has to be done. ‘And we better be ready to take it’.
Funny little man! exclaims the Phoenix as she darts around Wolverine. ‘I ain’t laughin’, darlin’!’ Logan exclaims, before asking the Phoenix why she just doesn’t finish it. Placing a hand on Wolverine’s shoulder, the Phoenix declares that she will - but not yet, and pushes Wolverine backwards. The Phoenix declares that she feels him coming, but that he is strong this time and has built a wall - he knows what has to be done.
The Phoenix declares that if she killed Wolverine now, then he would know it’s over and bomb her from the air. But she needs to see him, face-to-face. Look into his eyes. Wolverine lunges at the Phoenix, who declares ‘You can't die yet’ and holds him off with a powerful burst of energy.
Back in the X-jet, Archangel informs everyone that they are getting close to where he and Wolverine encountered the Phoenix, when suddenly they see the Shi’ar ship in front of them. Warren asks what they are doing here, but Scott declares that he doesn’t care so long they don’t get in his way.
Inside the Shi’ar jet, the helmsman reveals that he lost the Omega they were tracking, but there is something else below them in the forest. The commander realizes it is the Phoenix and orders ‘Fire!’ - only for the ship to be struck by lightning from Storm.
Down below, Wolverine and the Phoenix look up - as suddenly, a powerful blast crashes down upon them and the surrounding area.
In the X-jet, Cyclops asks what happened, Emma replies that Jean and Logan were down there, she had them for an instant. Hank reveals that there is a hole bitten out of the woods, like the bottom of a perfect sphere.
Inside the Shi’ar ship, the helmsman reveals that it was a direct hit and no trace remains. The commander asks about the other Omega and is informed that the signal is picked up again heading North. The Commander orders to move the ship North, when suddenly, telepathic images of Cyclops and Emma appear before him, saying ‘I don’t think so’.
The Commander tells the X-Men not to delay him, as the Phoenix has returned and the survival of the galaxy is at risk. Emma points out that he fired without warning on two X-Men and asks what his weapon was and what it did to them. The Shi’ar commander replies that they generated an Eleka’an Event Horizon, a miniature black hole, and declares that if they were caught in it, then they are gone forever. The commander is ordered to surrender this ship and personnel to the X-Men’s custody while they contact the Shi’ar Emergency Senate.
The commander states that he doesn’t have time for this and explains that the Omega is running North, pointing out that if traces of the Phoenix have survived, then he could become a host, so they must destroy him. ‘Will you aid us?’ he asks. Scott declares that they were prepared to destroy Dark Phoenix because they know what she has done, but that Quentin Quire is innocent. ‘relatively speaking’ remarks Emma.
The Shi’ar commander doesn’t believe there is any difference, and is about to explain what Quire could do as a potential host when Scott interrupts, exclaiming that by using the commander’s reasoning they should kill any mutant with psychic powers and omega potential. The commander just smiles, to which Scott tells him he is insane. Emma mutters ‘No, just typical little men with their big guns, always -’ she stops in her tracks, as she picks up a message from the Cuckoo’s who are in Cerebra.
The helmsman informs the commander that the X-Men are fleeing, to which he asks where too, but Nightcrawler and Storm teleport into the bridge - Storm telling the commander that it is not his return, before agreeing that Quentin Quire must be captured, but not killed. She asks the Shi’ar if they will help them, ‘Or should I tear this ship from the skies?’
Emma congratulates the Stepford Cuckoos, who inform her that Wolverine and the Phoenix are North.
The Phoenix, now in her green and gold costume, sits by Wolverine in the snow. Wolverine wakes, realizing that they are not dead, Jean asks him what the matter is. Logan declares that he knows she is using him as bait so she can get a hold of Scott. Jean smiles and tells Wolverine that is someone else’s plan, but she needs him for something else. ‘Something you’re the best at’.
‘You sure know how to use a guy up’ Logan remarks, before asking if she is Jean now, or still the Phoenix messing with his head. ‘I’m always Jean, and I’m always the Phoenix’ comes the reply, before she reminds Wolverine that she died, scattered in a trillion directions, before starting to pull together again, out of the White Hot Room, before admitting that she is beginning to see that parts of her never came home. The Phoenix / Jean declares that she is out of balance, and needs to try again.
The Phoenix pulls Logan’s fist towards her chest - and Logan shoves his claws into her. Wolverine manages to stand up, and looks down at Jean, blood all around her, when suddenly she rises, this time in the red and gold costume, Nice try she says, only for Logan to stab her again. But Dark Phoenix keeps rising, each time he stabs her she comes back, asking him How long can you keep doing this? ‘As long as I have to’ replies Wolverine. Their struggle becomes more intense, with Jean/Phoenix rising, and Wolverine cutting her down over and over again, eventually becoming drenched in her blood.
Finally it ends, Logan sits by Phoenix’s unmoving body. As he rests his head in his blood-stained hands, the Phoenix/Jean rises again - this time in the green and gold outfit. She congratulates Logan, telling him he did well, ‘She’s so much weaker now. Now I’m in charge’. With that, Jean flies up several meters in the air - before dropping down onto the ice, shattering it and plunging herself into the freezing waters below.
Soon, the X-jet lands. And the X-Men step out of it, Scott asking Logan where she is. ‘Dead’ replies Logan, ‘Or as close as she can get. She buried herself in the ice’. Scott asks Kitty for confirmation, and phasing into the ice, Kitty replies that she is on it. Down in the ice, Kitty sees Jean, while on the snow, Scott asks Emma what she senses. Emma replies that there is nothing down there, no brain activity at all. ‘Not even Kitty?’ asks Archangel. ‘Well, that hardly counts, does it?’ exclaims Emma.
‘Very funny’ mutters Kitty, giving Emma a filthy look as she phases back onto the land, revealing that it is Jean, in her green and gold costume, fifty feet down and frozen solid. ‘Kind of an anti-climax…’ she says, when suddenly Beast alerts everyone to the Phoenix raptor in the sky. Scott touches his visor, and despite Wolverine warning him not to, he fires. Logan reminds Scott that the Jean said she came for him, Scott pointing out that Jean knew what he would do.
But Beast tries to calm Scott down, explaining that Wolverine is right. Scott isn’t interested in listening, reminding everyone they agreed to attack. Beast manages to cut in and reminds Scott that the Phoenix feeds off stars, that it needs energy to survive - like the energy from optic blasts. As the raptor approaches, Beast declares that Jean didn’t come for Cyclops - the Phoenix did.
Don’t listen Scott…just open you eyes! declares the Phoenix as she lands on Cyclops.