Just outside the top floor of the X-Corporation building in Paris, three heavily armed helicopters hover menacingly. Through the amplified sound of a bullhorn, the lead helicopter informs the floor's occupants that they are surrounded and are instructed to hand over the terrorist Fantomex.
Standing with his back to the window, and the helicopter beyond it, Xavier holds a cellular phone to his ear. He tells his associate, Pierre, that he is sure that he and everyone else in the 18th arrondissement (district) heard the ultimatum. Further, Xavier tells Pierre that his staff is practically being held hostage downstairs. Drawing his attention to the wounded Fantomex, being watched over by Phoenix, Xavier tells Pierre that while it is becoming very clear to him that he is the most wanted mutant in Europe, the Xavier Corporation will not hand over a badly wounded man without a better explanation than "he's a dangerous man and must be destroyed ..." Xavier grows silent for a few moments as he listens to Pierre's response. After replying that he sees, Xavier thanks Pierre for trying and hangs up.
After solemnly looking at the phone he was just using, Xavier turns to Jean and Fantomex. Disheartened, he tells Jean that his friends in high places have realized there are higher places. Passing along what Pierre told him, Xavier tells Jean that they are apparently dealing with an "international strike force" sanctioned to capture Fantomex by any means necessary. Still bleeding from his left arm and abdomen, Fantomex tells Jean and Xavier that all he wants is sanctuary and a moment to catch his breath. Trying to examine the wounded man's arm, Jean asks him why they want him so much? Did he kill people? Steal?
Dismissing Jean's questions, Fantomex tells her that he's trying to concentrate as he's bleeding quite badly from a femoral artery. Suddenly, Fantomex looks at his arm in surprise. Examining it closely, he mutters that the bleeding has stopped. Looking back at Jean, he asks how she is doing that. Almost smirking, Jean replies telekinesis and says that she can make his blood clot by thinking about it. Looking back at Xavier, Jean says that she thinks they have to help him. Eyeing the still present helicopter outside, Xavier says he agrees. Staring intently, Xavier tells Jean that he is planting doubts in the pilots' minds. One boy is worried about his promotion; his heart is beating faster. The other is afraid that his collection of mutant pornography might be found by his wife. Sensing accomplishment, Xavier says that they are no longer sure what their orders were in the first place.
Sensing Xavier's complacency, Fantomex tells him to forget the mind stuff, as they will switch to robot targeting system. Undeterred, Jean states that she can think her way into the computer system. Replying no, Fantomex begins to stand, and asks Jean to keep her mind on his blood flow; he will handle this. Raising his arms and stretching them out toward the helicopter outside, Fantomex says that he has special powers too and he just needs to call his partner. The copter pilot has but a moment to wonder what is going on before a flash of smoke and light seem to consume the office containing the three mutants.
In the lobby far below, soldiers react to the apparent explosion at the top floor. One panicked soldier tells the others that the copter pilots are spacing out, which another blames on the telepaths who he says are everywhere. An officer, wondering if his thoughts are even his own, holds a phone to his ear and requests a volunteer with no mind of his own worth controlling. From the back of the group a lone soldier raises his hand and introduces himself as Corporal Animal. Walking through the rest of the unit, Corporal Animal tells his officer that he is a highly trained death machine with no human feelings. Sir! One of the soldiers Animal passes thanks aloud the Lord and the Marine Corps above for that and encourages the volunteer to do his duty.
Upstairs in the very much intact top floor office, Fantomex tells Xavier and Jean that it's all misdirection. Leading the two toward the exit, Fantomex tells them that they all look at the smoke and the lights, but they don't see what you're really... Fantomex stops in mid-sentence when he notices the towering form of Corporal Animal blocking the doorway. Holding his assault rifle in readiness, Animal guesses that they are wondering who he might be. Asking for them to let him tell them, the Corporal informs them that he is death in human form. Looking up at the threatening Marine, Fantomex tells Jean and Xavier behind him that as he's sure any one of them can handle this moron, this is the last chance for the pacifist lobby before he blows the man away.
Back in the lobby, the X-Corporation's mutant receptionist holds her branch-like arms above her head. Looking toward the marine whose rifle is pointed at her, she explains that he has a lunch date with a very famous French film star and asks if he is going to point that gun at her all day. Still aiming his rifle at the young woman, the soldier tells her to shut up and then adds that he really hates French movies. Nearby, the officer speaks into his phone and asks if there are any results upstairs. Just outside Xavier's office, several soldiers cautiously look inside. In the center of the office they see a downed soldier sitting with his head cocked to the side. Quietly, they ask the man if he is Animal. Not moving, the Corporal begins to ramble.
He tells them that when his daddy died, he was too young to make sense of it; he was just four. Turning around, Animal tells them that when you're a kid, you got no place to put those big old feelings, so he sort of stored up all the resentment about losing his dad right in his chest. Over time, he tried to be like his father, and became tough so the world could not hurt him. This made it difficult for him to make personal relationships. Looking now at the floor, Animal begins to wonder if he should reconsider his life with the military and begin to work with handicapped kids. Still standing in the doorway, one solider asks Animal what did they do it him.
High above, Xavier and Phoenix follow Fantomex to the roof of the X-Corporation building. Sitting amidst a protective smokescreen, is a giant sphere sitting atop four squatting insect-like legs. Circling the sphere at it's mid-section is a flat plane, which runs parallel to the ground. Pointing to the craft, Fantomex tells Xavier and Phoenix to meet E.V.A., his partner. After entering the craft through a luminous portal, the three mutants take their seats. Holding his head in disbelief, Xavier reels at the apparent flying saucer, remarking that he can barely get used to walking. Under the control of Fantomex, E.V.A. rises gently through the smoke to a point high above the city.
Sitting in her chair, an old, blind woman removes one earphone from one of her ears and asks aloud if it is Jean-Phillipe she hears. Holding a bag of groceries, Fantomex replies to his mother that, of course, it is he. Holding out a present, he tells her that he has brought her a new CD. It is the "Flutes of the Tibetan Damned". After pointing out that the sleeves notes are in French Braille, Fantomex notes to his mother that he always takes care of her. Sensing Xavier and Phoenix, Fantomex's mother asks him if there are people with him. Replying negatively, Fantomex tells her that it's just a play he's recording on the radio for her. Immensely proud, Fantomex's mother remarks how happy they are in their house, to which Fantomex agrees. Walking outside the house, Fantomex takes his guests to a stairwell, which rises into what would be the sky. However, instead of the sky, it leads higher into the monstrous structure in which the house has been build. Completely enclosed, the structure sits atop a mountain and provides a separate reality for the occupants to those who live outside.
On the top floor of the structure, Fantomex leads Xavier and Phoenix into a grand room. Ornately decorated, the room is filled with objects from a multitude of cultures and time periods. Sitting along the wall is a giant Egyptian stature of Anubis, suspended from the ceiling is a Viking boat, and sitting along another wall is a sarcophagus. Examining the décor, Xavier tells Fantomex that he'll try to ignore the deliberate strangeness of it all. Reclining in his massive chair made of spheres, Fantomex asks Xavier why ignore it? Embrace it! Taking control of the conversation, Xavier tells Fantomex that they did what he asked; they protected him from the mob. But, he continues, they are not in the habit of aiding and abetting self-confessed criminal terrorists. Cutting to the point, Xavier asks Fantomex what is happening to the X-Men in the Channel Tunnel and what is Weapon Twelve?
In the darkness of the Channel Tunnel, surrounded by the corpses of the Channel train's passengers, Monet calls out to her team. Calling to anyone who will respond, Monet asks what just happened? Rictor? Madrox? Siryn? Walking through the darkness, Monet finally sees movement. Unfortunately, the movement is from shadowy figures bearing glowing eyes and bared fangs.
Answering Xavier, Fantomex tells the two X-Men that Weapon XII is the latest in the series of living weapons tests being carried out by the military industrial complex. Bred in incubation units that speed up time itself, Weapons XII is created through artificial evolution to be the latest answer to the mutant threat. Through this process, mixed with sentinel microtechnology splicing genetic material, human scientists have run through a million years of cyborg mutation and development in eighteen months. Bringing the conversation back to the tunnel, Fantomex tells Xavier that the train wreck was faked. Monsters developed to kill mutants have been released and the Channel Tunnel situation was faked to set up to field test Weapon Twelve against a group of trained mutants. Being able to conveniently eliminate a number of asylum seekers was simply a perk. All of this, Fantomex tells Xavier is what he learned when he stole a dossier on disc from a research and development operation. If he wants to know more, Fantomex tells Xavier, the disc is for sale.
Dryly, Xavier points out to Fantomex that he could gift it to the Xavier Institute. Uninterested, Fantomex replies that he's a mutant with no scruples. Also, as Xavier's fortune is valued at 3.5 billion dollars and the Institute's teaching staff includes at least three millionaires, Fantomex says that he would prefer to sell. Bringing their subject to a more personal note, Xavier informs Fantomex that one of their close friends was designated Weapon X in this program, and was tortured. Unsympathetic, Fantomex mutters a mocking boohoo and then points out that it's Weapon Ten, not Weapon X. Holding up a disc, Fantomex tells Xavier that it includes all the details to the entire Weapon Plus program dating back to World War Two; all the failed experiments and the successes, the result of a thousand illegal tests on human, animal and mutants... like Mister Logan; for one billion dollars. As an after thought, Fantomex remarks to Xavier that he'd be interested to see how much money he'd be willing to sacrifice for his ideals. With this, Fantomex places the disc in a safe behind a framed poster.
As Fantomex calmly walks away, Xavier shouts that they need that data to know what they are up against. Sitting on a medical table, Fantomex begins to remove his torso vestments. Looking to Xavier and Phoenix, both of who has followed him, Fantomex tells them that he's read the Weapon XII file, and knows what he's up against. Angry, Xavier asks Fantomex if he's driven entirely by self-interest. Reaching for a medical instrument, Fantomex tells the professor that he would like to answer all of his questions, but he has to remove several bullets from his body. As he probes his own wound, Fantomex says that he prefers to self-operate, so he will be putting himself into a state of auto-hypnosis while his body works on itself. As he begins, Fantomex states that there's wine and a selection of fine French cheeses in the fridge. Asking them to make themselves at home, Fantomex tells the two that it won't take long.
Meanwhile, in the darkness of the Channel Tunnel, dozens of people run for their lives. As they do so, several of these people run over the fallen form of Monet, who is slowly regaining consciousness. Through her communicator on her wrist, Monet hears the voice of Darkstar calling to see if anyone is there. The fleeing crowd finally comes to a stop when they find a locked gate, and can proceed no further. Looking back from where they have fled, they see the approaching forms of wolves, accompanied by people not quite human. Finding their prey unable to run further, the wolves begin to tear the people apart. Elsewhere in the tunnel, Darkstar tries to protect another group of train passengers. In vain, she tries to calm the crowd. Their only response to her questions is "don't let them touch you." Through the darkness and mist, Darkstar sees wolves and other menacing forms approaching. As she calls out through her communicator for the rest of the team, Darkstar uses her dark force powers to repel her apparent attackers. Despite her efforts, they continue moving forward, step-by-step.
Looking out of his mountaintop home, Fantomex tells Phoenix that his mother thinks that they still live in their family home outside of Marseilles. He didn't have the heart to tell her it was demolished four years ago. Instead, he recreated it in the mountains. Watching Fantomex pour a liquid on his still cowled head, Phoenix asks him what he was trying to prove with his self-healing when she could have easily removed the bullets? And why won't he take off his mask? Replying simply, Fantomex says that he wanted to prove that he was serious. Also, he takes his mask off all the time, just not in front of her. With two telepaths around, he tells her, he prefers to keep his thoughts to himself. Wittily, he then asks Phoenix if she hears any complaints from him about her leaving her wonderbra on all the time?
Growing impatient, Xavier tells Fantomex that he's becoming concerned about his staff. Cross-armed, the Professor tells Fantomex that if he intends to return to the wreck, then he would like to travel with him. Anticipating this, Fantomex begins to back his weaponry. As he does so, Fantomex states that while he did humiliate their foes by stealing their data, he wants to make a much bolder statement against mutant vivisection. Even though he is brimming with self-confidence, he knows his limits; limits which are expanded with two of the world's most powerful telepaths running shotgun. Recalling his earlier offer to Xavier, Fantomex says that he was playing a little chess with morals. Now he is offering another difficult ethical situation: he will save the lives of the X-Men and everything else in Weapon Twelve's vicinity, if the two of them help Weapon Twelve itself. Not waiting for an answer, Fantomex dons his trench coat and strides toward the door. As he does so, he warns the two X-Men to not spend too much time deciding. Weapon XII must die.