Sunrise over the Xavier Institute for the Gifted, Salem Center, Westchester, New York. In their optic-blast damaged bedroom, Scott “Cyclops” Summers apologizes to his lover, teammate and co-headmaster, Emma Frost, the White Queen. ‘Sorry for what?’ asks the sultry White Queen. Scott pauses before telling her that he is sorry for having a dream about his dead wife that was so intense he broke his glasses and trashed the place with his optic blasts in his sleep.
Emma informs Scott that his heart beats every time he thinks about Jean Grey. Scott reminds Emma that Jean was his wife and that they never had a chance to say goodbye, because the ridiculous apocalyptic mind-blowing drama they went through year after year sticks with you. He tells Emma that as a telepath she should already know this, and know that he chose her.
Emma lies back on their bed as Scott asks her why they are fighting. Emma smiles as she tells Scott that she just wanted to hear him say it. Scott lies down next to her and declares that they are so screwed up. Emma agrees, and Scott asks if they are ever going to get better. The lovers sit in front of each other, and Emma tells Scott that she wants to see his face - all of it.
Emma uses her mutant power to transform into indestructible diamond as she pulls Scott’s ruby-quartz glasses off, Scott is hesitant, but Emma points out that as she is in diamond form, he cannot hurt her. Cyclops’ mutant power pours from his eyes, blasting onto Emma like a stream of water, and he smiles as they look into each other’s eyes. Emma tells Scott that he has beautiful eyes, before they kiss.
But soon, Scott pulls away, something is wrong, as Emma is so cold. Emma apologizes, and tells Scott that it was a nice idea, but that in her diamond form, she cannot feel it. Scott puts his glasses back on, and Emma returns to her human form, asking Scott if he wants to try again. They start to kiss again, and Emma uses her telepathy to enter Scott’s head. Emma asks him if he minds, Scott replies that he doesn’t, that it feels nice, but warns her that she is probably going to see some stuff she doesn’t want too…but its too late.
Emma tells Scott that it is all right, she knows he cannot help where his mind wanders to. Scott tells Emma that she is the best, ‘Don’t push it,’ Emma replies. Scott reveals to Emma that Jean once held back his optic powers with her powers, and suddenly, Scott begins to think of Jean. He thinks Emma is doing this and tells her not to, but Emma informs him that these are his thoughts, not hers. Scott exclaims that he doesn’t want this, that he wants Emma. Emma asks him why he looks so sad, and why he only sees her in her diamond form.
Cyclops and Emma separate, Emma telling Scott that she thinks he only loves her because she is hard and cold and mean. Scott says ‘No…’ but Emma tells him that all he wants is a woman he can’t hurt. Scott tells Emma that at this point, Jean would have blown a hole in the wall and flown away, but that she sticks around. He tells Emma that she bugs him, drives him crazy, pushing him places he doesn’t want to go, but knows he should.
‘You’re good for me, Emma Frost. That’s why I love you,’ Scott says. Emma smiles and tells Scott that now he is going to make her cry. ‘Kiss me again,’ she says, when suddenly, Wolverine jumps into their room, ‘She’s back!’ is all he says.
Soon, Cyclops, Emma, Wolverine, Beast, Shadowcat and former X-Man Archangel approach the graveyard, specifically the grave marked “Jean Grey-Summers, She Will Rise Again”. Archangel a.k.a. Warren Worthington the Third suggests that this maybe some sick joke, or someone might have dug Jean up, but Wolverine, a.k.a. Logan declares that he saw her. Warren asks what the plan is, and Scott quickly replies that they find her and destroy her.
‘Dude, I think your baggage is showing,’ Kitty “Shadowcat” Pryde tells the senior X-Man, who turns to Kitty, ‘Excuse me?’ he asks, taken aback. Kitty tells Scott that his wife is back barely an hour and suggests it may be a little early to be burying her again. Scott tells Kitty that Jean is not back, to which Warren reminds Scott of what he said some moments ago, but Scott raises his voice and says that it is not Jean.
Wolverine tells Scott that he did not only just see Jean, but he smelled her, so it is definitely her. Dr. Henry McCoy a.k.a. the Beast sniffs the air and agrees, saying that Jean was here, and alive. ‘No!’ replies Scott again, before Kitty turns to Emma, and addressing her as “Miss Frost” asks her what is going on. Kitty scowls when Emma derisively says ‘Call me Emma, Katherine, its ever so much nicer between friends’.
‘Enough!’ shouts Scott, reminding everyone that he and Jean were psychically linked, but that their connection ended when she died, and while she has been on his mind, she has not been in it. He tells Logan and Beast that they may be smelling her body, but she is not in it. ‘She’s dead’. Wolverine suggests that Jean may just be protecting Cyclops, as he heard the Phoenix Force inside his head.
Logan reveals that the Phoenix Force said it came here for Cyclops, and that Jeannie was fighting it, trying not to let it take over. Logan agrees that they have to kill the Phoenix Force, which is why he thinks Jean brought it to him in the first place. But Logan is not going to pretend that this is Jean’s dead corpse walking around, this is actually Jean, living and breathing and fighting away like a champion.
Everyone stares down at Jean’s grave with a moment of silence. Kitty glances sideways and declares that even if this is the Phoenix, she doesn’t see how they can go intro this with killing her off as their first plan of attack. Scott asks Logan what happened to his torn clothes, and the handsome X-Man replies that the Phoenix torched him. Scott asks what color costume the Phoenix was wearing when she torched him. ‘The red ‘n’ yellow one’ replies Logan. Scott asks Logan how many people died last time she was wearing red and yellow. ‘Bout five billion’ Logan replies. Scott turns to Kitty, and tells her that this is not “Phoenix”, but Dark Phoenix!
Cyclops declares that there is no time to waste, and sends Logan to track Jean’s scent from the ground, while Archangel searches from above. He tells them not to engage her, just to report back the instant they find her. Cyclops tells Emma, who is in Cerebra, to search for any telepathic sign of the Phoenix, and to spread the word to any X-Men in the field, and to ask about any anomalies, or strange energy patters. ‘Giant firebirds in the sky?’ suggests Emma. Scott tells Emma to tell the others not to engage the Phoenix, just to report back with the location.
Cyclops tells Beast that he knows he would rather by running with Wolverine, but he needs him in the lab, and asks him if he remembers the device he made last time to block the Phoenix’s powers. ‘The headpiece?’ asks Hank. Scott points out that it got friend pretty quick, so tells the Beast to make it better and bigger, something they can trap her inside even. Scott tells Kitty to get Colossus and prep the X-Jet, as they are going airborne the instant they get any word.
‘And what are you doing, fearless leader?’ asks Emma, smiling. ‘Fearlessly leading, of course’, replies Cyclops, now in uniform as he searches the forest surrounding the Xavier Institute.
‘Jean?’ shouts Cyclops, turning quickly when he sees a female figure emerge from behind some trees. ‘Nice reflexes’ says Emma as she reveals herself. Scott thanks her before she gives him an update: Storm has found an ultratropical storm in the North Atlantic which she says feels all wrong. Scott asks Emma if she got a reading, and Emma replies that there was no Phoenix energy signature and no sign of Jean if that is what he is meaning, when suddenly, Emma sees Jean flying towards them, and shouts ‘There!’
Cyclops fires a powerful optic blast, knocking Jean / the Phoenix backwards and into the containment egg that Beast had designed and built. Scott! No! cries the Phoenix as Beast closes the lid on the containment device.
Soon, deep within the Xavier Institute, the Danger Room returns to neutral as Hank comments to Scott that everything went well, to which Scott congratulates Hank on a good job and tells him to get back to finishing that containment egg for real. Beast replies that he will, before asking Scott what he is going to do. Scott declares that he is going to run the simulation again, to which Beast points out that there is no way he can really train for this, that they have no idea of what kind of terrain they will be in.
Cyclops reveals that he is not training for the terrain, but that he is trying to get used to killing his wife. Suddenly, Emma telepathically calls to Scott that she detects an Omega level mutant, adding that this is not a drill. When Scott asks ‘where?’ Emma replies ‘In the mansion!’
Beast leaps through the mansion, past students, watching in awe as he rushes towards his lab, where telepathically, a nursery rhyme, “Humpty Dumpty” is being projected. ‘Oh my stars and…’ begins Beast, not getting to finish his trademark saying as he enters his lab and a holding tank explodes before him.
Elsewhere in the Institute, three identical blondes - Celeste, Mindee and Phoebe, known as the Stepford Cuckoo’s unanimously exclaim ‘He’s back!’
Beast stands before Quentin Quire, a.k.a. “Kid Omega” who is dripping with goo from the exploded tank. Quire asks Beast where Sophie is. Beast begins to explain what happened to Sophie, when Quentin touches Beast on the head and begins to read his mind, for he can feel Sophie’s presence, feel her power - but when he sees in the Beast’s mind that Sophie has died, he declares that the Beast is lying and declares ‘Stop moving, nobody move!’
All through the Institute, everyone is frozen in their tracks. Beast opens his thoughts to Quentin so that he can read his mind, telling Quentin that this is not very nice. Quire tells Beast that he is not listening to him as he is clearly insane. Beast tries to get Quentin to talk to him, but the young mutant blocks his ears and keeps repeating ‘I can’t hear you…’
Throughout the Institute, frozen students wonder what is going on and why they cannot move, when suddenly, the see Kid Omega walk past them. Hiding in their room, the Stepford Cuckoos tell each other to not think, to empty their minds as Quentin cannot find them if they don’t - but it is too late as Quentin enters their room, calling to Sophie, he declares that Dr. McCoy said some confusing things - but Quentin looks at the three blonde girls and doesn’t see Sophie. He understands now that indeed Sophie is dead, and unleashes a burst of energy that blasts out of the Institute.
Elsewhere, Ororo “Storm” Munroe soars through a cloudy sky, with her good friend and teammate, Kurt “Nightcrawler” Wagner following on a airborne vehicle. Kurt tells Storm that there is no answer from the mansion, so Ororo tells him to keep trying, adding that this storm is moving all wrong. ‘Hurricanes have a right way to move?’ asks Kurt, before Storm reminds him that she feels this planet, knows the gravitational pull of the moon, the rhythms of the winds and tides, that a normal hurricane fits into all that, but this one doesn’t.
Storm simplifies it, explaining that in the Northern hemisphere, the storm should be spinning counter-clockwise, but that this one is going the other way. Storm believes there is something driving this storm, and tells Kurt that they need to get Cyclops on line again. Kurt replies that they are not answering still, and fears that something has gone terribly wrong at home.
Somewhere above, the helmsman of a Shi’ar vessel informs his Commander that thirty seconds ago, an Omega-level energy form was detected in the New York area. The Commander orders ‘Fire when ready’, but the ship’s counselor protests yet again, reminding the Commander of the Emergency Senate Decree, that they must not interfere with this planet.
The Commander reminds the Counselor that the Empire is broken, that the Phoenix may be injured now, but an Omega mutant could be a host, or give it the strength it needs, that neither risk is acceptable. The Helmsman alerts the Commander, motioning to the view screen, which Storm has trapped the Shi’ar ship in the hurricane. ‘Hello, sunshine’ she says.
The green energy form of Quentin Quire flies towards the graveyard at the Xavier Institute, and enters the earth surrounding the grave labelled ‘Sophie: One of Five; Heroine of Open Day”. ‘There you are!’ Quire says upon seeing the skeleton of Sophie.
Meanwhile, Archangel tells Logan that Emma has stopped checking in and that no one is answering any cell phones. He begins to ask Logan what they should do, before asking Logan, who keeps running through the forest, if he is listening. Logan doesn’t reply, so Warren asks him what he is looking at, but Logan tells Warren to go back to the others and tell them that he has got her. Warren calls out to Logan, but Logan runs deeper into the forest, and lunges at a bright emerging light. ‘Hello again!’ says the Phoenix.
Back at the graveyard, Quentin Quire has pulled Sophie’s body from the ground, muttering that he is sorry, that he remembers all the blood now, that he was stupid…’I just wanted you to like me1’ he says as he places a hand on Sophie’s arm.
Quentin mutters ‘Stupid little bug’ and that he thought it would help him, he thought it came for them. Tears streaming from his eyes, he suddenly realizes that it came for Miss Grey, and noticing her grave, obviously brought her back. Picking up the body of Sophie, he powers up, he declares ‘Let’s see what the Phoenix can do for us!’