Standing behind a podium, an austere man in a suit addresses his audience. Starting off simply, he introduces himself as Charles Xavier and admits that he is a mutant. He tells his audience that the doors of his international X-Corporation offices are now open and asks them to consider them a worldwide refuge in time of trouble.
In counterpoint to Xavier's words, outside the building housing his speech, a group of mutants are under siege. A mob of anti-mutant zealots have chased over a dozen obvious mutants and corralled them behind the safety of an iron fence surrounding a statue monument. As the mutants try to defend themselves as best they can, Xavier tells the mutants in the audience, and those around the world, to simply think of the emergency "X" and they will register on their Cerebra machine. Once registered, trained X-Men will be on hand to help them. As if to illustrate Xavier's words, a team of X-Men consisting of Cannonball, Darkstar, M and Siryn drop out of the sky to the rescue.
Later in the X-Corporation building in Paris, Phoenix congratulates her group. As the team changes into fresh uniforms in their locker room, Jean tells them that from the ashes of the X-Corps debacle they are making a public relations comeback. Examining his costume, Rictor makes a disparaging comment about the X-Corps. Putting on a new shirt herself, Siryn tells Rictor to see her stupid dad for starting it all. She then adds that she's there to atone for his sins. Noticing Jamie Madrox, the Multiple Man, holding his forehead, Jean inquisitively states that he doesn't feel well. Straining under obvious pain, he replies that one would think that he would be able to divvy up his hangover among all of his duplicates. No such luck. Sitting next to Madrox is one of his duplicates, who pops an aspirin and asks whose idea it was to have an emergency mission the day after they all go mental on the dance floor.
Now finished dressing, Siryn asks Jean what is the next gig. Looking over Jean's shoulder to her notes, Monet answers for Jean, telling the group of a train wreck in the Channel Tunnel. The wreck left one hundred twenty passengers and thirty asylum seekers trapped. Continuing on her own, Jean tells them that the Professor's contact in London mentioned a potential gene-hazard on the train, which is why the X-Corporation Europe got the call. As the team makes their way to the roof, Jean explains that because of the hazard, they have to get the people out of there before anyone else gets hurt. Reaching the roof, Jean mentions that Siryn wanted to talk about codenames. As the non-flying members enter the X-Corporation's aircraft, she asks if they can all use their school nicknames instead of the "daft, ponsy 'gladiator' names". Considering the idea cool, Cannonball mentions that the name he was called for five weeks as a kid, "Jet-Ass" is much better than Cannonball. As the craft and the rest of the group take to the air, Darkstar says that she wouldn't mind changing her name. Monet, ever dry in humor, informs her teammates that she was bullied at school and will stick with Monet, thank you very much.
From his office in the X-Corporation building, Xavier and Jean look out over the city. Having stretched his mind out to the city, Xavier tells Jean that there is a young man in Montparnasse who is thinking about how cool those X-Men looked on TV. He tells her that it is hard to believe, but they are finally listening to them. As Xavier continues his gaze outside, Jean walks back to the nearby chair. Continuing, Xavier says that all they had to do was to take off their frightening masks and step from the shadows. Sitting down, Jean replies that combining the goodwill tour with a branding exercise has led to their having a list of mutants all begging to volunteer for work at the X-Corporation offices. On the table before Jean, a glass and a bottle of Perrier water begin to float, seemingly of their own accord. Methodically, the cap unscrews itself and the bottle approaches the glass. Turning on its side, the bottle pours its water into the glass, and then repeats the maneuver into a second glass. Still looking outside and lost in contemplative thought, Xavier voices his disbelief that he's been able to leave Emma, once a sword enemy, in charge of the school. When Xavier comments that Emma has been a revelation, Jean quietly "hmphs" to herself. Not hearing Jean, Xavier admits that it's been a long time since he's felt this good... or this nervous. No more need to hide their mutant natures. No more human rules.
Hearing this, Jean tells Xavier to watch it; he sounds like Cassandra Nova. As one of the glasses of Perrier floats to his position, Xavier admits that Cassandra was right to go on television and break their silence. She was right to reveal them to the rest of the world. She took the step he always knew he had to take, but he always found an excuse not to put his reputation on the line. In trying to do evil, Xavier says, she freed them from their self-imposed exile. Finally noticing the glass of mineral water floating at his side, Xavier plucks it out of the air and thanks Jean. He then apologizes for his ramblings and brings them back to the reason for their meeting: Jean's desire for him to take a look at the growing power source in her skull. Reclining in her chair with her arms crossed behind her head, Jean tells Xavier that everybody at the school seems terribly worried about her expanding telekinesis. Basically, she tells him, she needs him to tell Scott that she's not turning evil.
Along one of the old, narrow streets of Paris, five special ops military soldiers are tracking someone. One of the soldiers at point exclaims that their quarry has gone to the right, and begins to lead the rest. Finding their path dead-ended by a metal gate, they begin to argue about calling the chase off and returning home in time to watch the European Cup final. With his pursuers distracted, the soldiers' quarry drops from his perch high above. His guns at the ready, he begins firing at the soldiers, taking them out one by one. Unable to take them all, the masked man jumps the metal gate, stating that there will be no Cup Final today. As he makes his escape, the masked man is hit with a stray shot.
In a X-Corporation office, Xavier and Jean sit across from each other with only a glass table between them. As Xavier sets a briefcase on the table, Jean explains her situation. She tells him that it's like she's seeing more of everything, but it all melts together. It's not just sight and sound, it's like all of her senses are rippling through her surroundings. Noting the briefcase, she fingers the latches. As she opens it, she asks Xavier if he thinks she is nuts. Dismissing this, Xavier tells her that the briefcase is simply an experiment he has devised using the very expensive dining set someone ordered for the staff canteen. As Xavier says this, Jean looks at the contents of the briefcase: a very expensive set of cutlery. As Jean studies the silverware, Xavier explains that when he was dying, she held his consciousness together. Even though he did lose a few memories, what she did was impossible; the storing of a human mind intact. Even for an omega mutant, Xavier says, her feat should not have been possible. Closing her eyes, Jean tells Xavier that if she can think it, it's possible. Telling Xavier she is ready, Jean begins to lift telekinetically all of the cutlery into the air. One by one, she arranges them into a circle. Even though Jean considers this a test for beginner telekinesis, Xavier believes that there could be more to it. On a hunch, Xavier reaches out and gently touches a fork floating before him, asking Jean if she can feel it. Amazed, Jean responds that she can and says that she didn't know she could do that. As little flames begin to appear in her hair, Jean exclaims that she can feel his pulse through the stainless steel.
The circle of cutlery, previously aligned in the air perfectly, begins to fly in multiple circles. Sitting before this aerial display, Xavier tells Jean that telekinetic sensitivity this extreme is known as the Manifestation of the Phoenix by neuro-mystical surgeons of the Shi'ar Space Empire. He also reminds Jean of the great trials the X-Men underwent during a previous rogue Phoenix manifestation and coldly states that no one wants anything like that to happen again. Her hair now aflame, Jean tells the professor that she knows, but it's nothing like that. She tries to voice what she sees, explaining that it's like colors on fire, burning in every direction. Tapping into Jean's psyche, Xavier replies that he feels it. It is like he is on the shores of what seems an ocean of psychic light. If he actually dared to come any further into her consciousness, all his thoughts would turn to ash. Leaning forward in his chair, Xavier looks hard at Jean and asks bluntly if he can talk to the Phoenix. With a voice not her own, Jean replies that Jean is only the house where she lives.
Suddenly, Xavier finds himself and Jean no longer in the office, but in the rubble of a city in ruins. Still speaking to Xavier, the Phoenix Entity tells him that it is born and consumed in blood and flame and sacrifice; always coming back. Referring to the carnage and destruction around them, Xavier asks Jean what is this place? Are these words from the future? What is happening? As quickly as the new reality surrounded the two, Xavier and Jean are back in the X-Corporation office. The Phoenix Entity, replying to Xavier's queries, explains that it's not a place; it's how it feels to be the last hope and to know you'll win against all the odds. It's the wing of the Phoenix touching your heart with flame. Taking all of this in, Xavier rubs his eyes. As he does so he tells Jean that his mind feels blinded and dazzled, and asks if she is all right. Looking up, he asks Jean why she looks so strange. Fully restored in mind, Jean looks in horror at something behind Xavier. Through the window to Xavier's back, an airborne craft has appeared. Pointing to the menacing and armored black helicopter, she asks what it is doing there.
From the shadows a voice apologizes and answers that it's he that they want. Xavier and Jean turn in surprise to the origin of the voice. They see a masked man emerge from the shadows. He is clad in an all white body suit and coat, stained with blood from several gunshot wounds; wounds he received earlier from his altercation with soldiers. The stranger tells them that he can read body language, so he knows that they're wondering how he got in and why they only see white roses when they try to look inside his mind. Pointing to his cowl, he tells them it's made of thought proofed ceramic panels. Emerging from the shadows, the man says that he heard Xavier's speech on TV and decided to put them in a morally compromising position. He tells them that he is asking them to harbor the most notorious mutant criminal in Europe. Introducing himself as Fantomex, he tells them that he is a mutant and demands sanctuary.
Near the Channel Tunnel entrance, the X-Men team arrives. As he lands, Cannonball voices his regret that he ever ate that sandwich. Darkstar adds that everyone without an umbrella in downtown Beauvais regrets it as well. Talking to one of the already arrived Madroxes, Siryn asks if that was he who was trying to sing "Justify My Love" and declares that it was the most perverted thing that she has ever heard. When the conversation moves to possible sexual practices by Madrox by himself, Monet requests that it stop and asks for an update on the Tunnel situation. Madrox replies that he hasn't seen anyone and then asks Cannonball if he really threw up over Beauvais.
Looking out the window down to the street below, Jean sees the gathering of military forces. She tells Xavier that they have been surrounded, and that the forces below have orders to bring in their guest at any costs. Tapping into their collective minds, Jean says she's they are terrified of Fantomex because they don't know what he can do. Taking a cup of water offered by the professor, Fantomex tells the two that he is a thief and stole something that he shouldn't have. Something big and bad got loose in the train wreck; something called Weapon XII. Pouring the water onto his still cowled head, Fantomex informs Xavier and Jean that their emergency team is probably already dead.
In the Channel Tunnel, the X-Men emergency team find themselves under attack by the very people they were planning on rescuing. Being pulled down by several of the passengers, Madrox yells for the team to fall back. Crying aloud about the hundreds of attacker, he yells for the team not to let their attackers touch them. He is able to repeat the order once more before his world enters darkness.
In a darkened room, illuminated partially by shafts of sunlight, two chairs sit; one occupied the other not. From the shadows, a voice admits supposes that he just wanted to talk to somebody about Jean and he. Emerging into the light, Cyclops takes the seat. He tells his confidant that through all the death and horror and wonder they've seen, he's trying to hold onto that shining, unmistakable thing they felt once on the moon together when he thought he'd lost her forever; but it's phony. He admits that they were faking this teenage, uncontrollable love in the face of unstoppable chaos and change. Cyclops says that while he still loves Jean more than his own life, he is not who he was and can't seems to tell her who he is ... in case she hates what he has become. Leaning forward, Cyclops says that he can save the world a dozen times before breakfast, but can't talk to his wife about the stuff that matters most. Looking at his feet, he tells his listener that he guessed that she could help. Finally speaking, Cyclops' confidant tells him that he's been keeping rather a lot bottled up. Reclined in the side of her chair, Emma Frost tells Cyclops that he came to her just in time.