In the darkness of the Eurotunnel, Siryn, Rictor, Cannonball and a cadre of Madroxes fight for survival against the glowing-eyed thralls of Weapon XII. Calling to Madrox, any of him who will listen, Siryn asks what is plan B? Trying to avoid the swoops and strikes of airborne ravens and bats, a number of Madroxes voice one word each their answer: we... have... no... plan... B... Siryn. Seeing a need for change in their strategy, Siryn yells to her teammates to cover their ears if they don't want this to be the last thing they hear. With her teammates sufficiently warned, Siryn emits an ultra-sonic scream, which knocks back a wave of possessed tunnel train passengers. Now granted a brief respite in their battle, the strike team turns toward the French end of the tunnel and begins to run. As fast as they are already running, Madrox urges them faster after seeing the towering form of Weapon XII approaching. Holding up the rear, Cannonball thinks of his other missing colleagues, Monet and Darkstar. Where are they and what is the team up against?
High above Paris, Fantomex pilots the craft called E.V.A. toward the channel tunnel. With his head covered by the organic tendril of E.V.A., Fantomex manipulates a corresponding sphere with his free hands. As he does so, he explains their situation to Xavier and Phoenix. The Weapon Plus program, he says, was an attempt to create supermen to fight future wars. Weapon 0 was classified and Weapon I was a volunteer program. Weapons II through III were animals and Weapons IV to VI used various ethnic minorities. Then, for the Weapon VII trials and onwards, they discovered the ideal subjects; kidnapped mutants, the scum of the Earth. Repeating what he said earlier, Fantomex tells the two X-Men that Weapon X wasn't a letter; it was a Roman numeral; ten. Mister Logan, he continues, was only the tenth generation living weapon. They've gone far beyond that now. Weapon XII, he says, can become his enemies, or more accurately, they become him. He is a soldier who recruits just by touch.
After a vain attempt to divert this discussion back to the X-Men, and who knows how many innocents, trapped in the tunnel, Xavier makes an offhanded remark about Fantomex's ship. Quickly, Fantomex corrects Xavier. E.V.A isn't a vehicle. She, he says, is his partner. His mutation. Holding his thumb and forefinger a few inches apart, Fantomex states that she was only this size when she emerged from his mouth the day his voice broke. From his seat in the back row, Xavier reaches out to a section of the ship within arm's length. Reaching out with his mind, Xavier states that he can sense her aliveness now... pure machine consciousness. Likewise touching a section herself, Phoenix states that she seems friendly and asks what happened. Fantomex replies that he used to keep her in a birdcage and feed her Swiss chocolates. It was years, he says, before his pet saucer began to talk to him. Fantomex's story abruptly ends with the three's arrival at the Eurotunnel. Reaching out telepathically to the tunnel, Phoenix asks Xavier if he can feel it. Doing so, Xavier asks Fantomex if this is what he was talking about. As E.V.A. descends to the tunnel's entrance, Fantomex tells Xavier, yes; Weapon XII's mind spreads like a disease into whatever it touches.
In the darkness of the tunnel, one of the Madroxes looks up at the illuminated form of Weapon XII. The towering mutant bares his razor claws and beads down with his incandescent eyes. Sprouting from his head like a glowing plant, Weapon XII's powerful brain pulses with energy and power. Standing nearly beneath this massive form, the Madrox informs it that if it needs help, they're there to help mutants in trouble. Reaching out with his powerful limbs, Weapon XII sinks his talons into the sides of the Madrox's skull. As the Madrox screams in pain, Weapon XII, in halting speech, tells Madrox that he is the one in trouble. After Weapon XII releases him, the Madrox does not fall, but instead turns around to face his fellow duplicates; but now with glowing eyes. Another Madrox looks in horror at what has happened to his fellow duplicate. Analyzing the change in his fellow dupe's mental rapport, now Madrox senses Weapon XII's voice; eating him, thinking his thoughts. Nearby, another Madrox realizes that Weapon XII is a bacterial consciousness while yet another announces that everything he touches spreads his thoughts.
Trying to reconcile this new information with their situation, Cannonball hopes aloud that the silver flying saucer out there's on their side. From within that same saucer, Professor Xavier tells Jean, now ! Back in the tunnel, the legion of Weapon XII thralls halt their forward movement. Taking advantage of the respite, the strike team doubles their pace toward the exit.
Still in her seat, Phoenix concentrates intensely as small flames dance about in her hair. To Xavier, she states that she's got it, though she doesn't know what it is. She continues, stating that she's suspending its motor functions, but doesn't know how long she can keep it up. Its mind, she says, is like a bag of worms, weird, bending around her mind. Rising from his seat, Fantomex warns Phoenix to not get too wrapped up in his thought processes. They are entirely viral. Wincing in pain, Phoenix states that it's adapting to her attack. Millions of little brains... all thinking at once. Having landed E.V.A., Fantomex opens the exit portal. Looking at the train tracks below, he tells Phoenix that she can probably paralyze it long enough for him to finish this. The off-switch, Fantomex informs them, is in the train that was transporting it. They couldn't risk the experiment getting completely out of hand.
Having exited E.V.A., the three mutants stand at the mouth of the tunnel and greet the escaping strike team. As she checks out the group, Phoenix is surprised to learn that Rictor has a kind of natural psychic defense against Weapon XII's infection. Nearby, Xavier congratulates Cannonball, crediting him with saving Siryn's life. Ever humble, Cannonball responds that it's his job and then adds that he thinks he can do more. Addressing the young X-Man as Sam, Xavier tells him that they will call him if they need him. Pointing to the outside, Xavier says that with Siryn's vocal cords bleeding badly he first wants him to get her to safety.
As Cannonball flies Siryn away in a blast of fire and smoke, Madrox approaches Xavier's guest, Fantomex. Offering his hand his friendship to Fantomex, introduces himself only to have Xavier's guest respond, "good for you". Turning toward the tunnel, Fantomex calls out the name Zona. When asked who Zona is, Fantomex answers that he's the guy with the "external brains". Zona, actually Zona Cluster 6, Fantomex explains, had a life in the real world before the program twisted him into a super evolved killing machine. As the mind controlled thralls of Zona begin to emerge from the tunnel, Fantomex tells the X-Men that they must kill him before he can be returned to his life pod and debriefed. Running at a sprint toward the emerging enemy, Fantomex clarifies: he has to kill him now. Her hair now alive with dancing flames, Phoenix runs after the charging mutant terrorist, yelling that there are still people trapped in there!
Watching in horror, Madrox yells for Jean to stop. Turning to Xavier, Madrox tries to explain that the enemy is contagious, with hundreds of infected people and animals. Inside still, he says, are Darkstar and Monet... Xavier tries to calm to hysterical Multiple Man, telling him that it is all right; he is being relieved of duty. Placing his hand on the shoulder of the visibly exhausted youth, Xavier tells Madrox that he believes he can beat Weapon XII at his own game, without further bloodshed. All he needs, Xavier tells him, is to borrow his nervous system. Looking up at his leader and mentor, Madrox replies that it is no bother and he doesn't even have to try to explain it. All he needs is a little rest. Placing his hands on Madrox's temples, Xavier tells him to rest; he deserves it. As Madrox's eyes go all white, Xavier softly tells him that he will take telepathic control now.
Illuminated in the darkened tunnel by the burning wreckage of the train, the possessed passengers of the Eurotunnel train await the approaching Fantomex and Phoenix. Not slowing in the least, Fantomex draws his two handguns and fires at a full run. Those thralls not mowed down before his arrival, are dispatched as the mutant terrorist leaps overhead, firing from above. Fantomex's leap comes to a stop with a controlled drop and roll maneuver. Rising back to his feet, the one-man combat team snags part of his cowl on nearby debris, partially removing it. Still not missing a beat, or taking the time to fix his cowl, Fantomex continues his firing, unleashing silver-white bullets with ghostly images on their tips. Having taken out the last of the apparent thralls, Fantomex stops firing and surveys the situation.
Next to the derailed train, M and the uninfected passengers within look at Fantomex in horror. Calling the white trench coat clad mutant a lunatic Matrix freak, M exclaims that the last person he has killed was Darkstar. She was a super hero. Still bearing his weapons, Fantomex retorts that she stopped being human the instant Weapon XII touched her. And, he tells M, judging from her lack of genuine concern in her vocal modulation and body posture, he deduced that she was only some girl she never cared much for. An associate at best, right? Dumbstruck, M can only respond that they were standing there in the middle of this and... she didn't get the chance to make friends. Examining an open containment pod, Fantomex coldly retorts that she never will. Life is tough. Now as Phoenix is buying her time, he suggests to M that she use it to do her job as a rescue worker.
Standing in the mouth of the tunnel, Xavier, surrounded by scores of Madroxes, calls out to Weapon XII and introduces himself. Emerging from a side tunnel, the towering incandescent Weapon XII reveals himself. Announcing that he was born to make war on the mutant race, he asks has war begun? Is this war? Has war begun? Striding with colossal steps, Weapon XII and his thralls make their way toward Xavier. Within steps of the professor, Weapon XII and his minions are met by the scores of Multiple Men. Clawing at the wall of Madroxes and infecting them, Weapon XII commands his new agents to make new world for man; make war in the name of eternal man. Concentrating on all the minds of the infected Multiple Men, Xavier replies that this isn't war. Speaking now through the numerous infected Madroxes, he tells Weapon II to call it medicine, if he likes. His own mind now vulnerable through the recently possessed, Weapon XII's face contorts in visible agony and a silent scream.
Arriving at the derailed train, Phoenix finds M assisting the uninfected passengers to the ground. Informing the young X-Man that the way is now clear, she tells her to get the survivors out. Still shocked by the carnage around her, M stammers out that everything went nuts... and he killed Darkstar. The calm and collected antithesis of M, Phoenix explains that it wasn't her anymore. Next, trying to keep M's mind on the present instead of the past, Phoenix tells her to take it easy and walk toward the floodlights. This taken care of, Phoenix turns her attention to Fantomex and the containment pod he is inspecting.
Finding several component pieces, Fantomex's methodical search is interrupted by the questions of Phoenix. She tells him that she hates to bring this up, but if there was only one Weapon XII, then why are there two cages? After the telling silence and stray thoughts from Fantomex, Phoenix comes to a revelation. Telling him what he already knows, Phoenix tells him that the second pod was his pod, wasn't it? And everything else was a lie... that's why they never heard of "Fantomex". Holding a hand-held detonation switch with a thumb-button, Fantomex rises to his full height. Fixing his thought-proofed cowl, Fantomex realizes his situation and rhetorically asks if their minds are leaking, aren't they? His cowl replaced and his mind re-secured, Fantomex tells Phoenix that they dipped them in liquid time; injected them with micro-Sentinel machines. The world, he tells her, is smaller than this one. Its rules and its people are very different. While Zona turns his enemies into himself, he is much smarter than they bargained for. He won't be anyone's soldier.
Stepping closer to him, Phoenix asks Fantomex to not tape up his thoughts. It was just getting interesting. After a beat, she asks him if there is no European super-thief, is there? There is now, he answers. Illusion and misdirection. He, he tells Phoenix, is a new form of life and this place is so much more fun than the world in the Weapon Plus Program. Reeling at Fantomex's connotations, Phoenix asks about the house in the mountains? Who was the old woman? Pressing the button on the hand-held detonation switch, Fantomex asks, what old woman? Elsewhere in the tunnel, surrounded by the scores of Multiple Men, Weapon XII's head explodes in blue light.
As the corpse of Weapon XII collapses to the ground, so do his thralls, killed by proxy. More curious than surprised, Xavier asks the Multiple Men if they did that? Did he think too hard at Weapon XII? Surveying the scores of bodies, the Multiple Men state the obvious; everybody's dead. Stroking his jaw, Xavier states that he was rather hoping they could avoid this pointless, brutal solution. Examining the pseudo-skeletal remains of Weapon XII's skull, Xavier remarks on it's bizarre, branching brainstem system, comparing it to coral. Arriving from the tunnel's depth, M leads the train survivors. Still unable to regain her composure, she tells Xavier that Jean is still in there with some gun nut who shot Darkstar. She's dead. Otherwise, she says, mission accomplished.
Lies, Phoenix tells Fantomex. Dropping the detonation switch, Fantomex begins to search his trench coat pockets. Defending himself, he tells Phoenix that Weapon Plus is the real, the world is real, but there's no dossier, no disc. The secrets of the program, he says, is here, in his head and available at a price. Holding a new detonation switch freshly pulled from his pocket, Fantomex informs Phoenix that it is his, now disabled. Pointing deeper into the tunnel, Fantomex tells the X-Man that England is that way down the track and the tilt of her pelvis tells him that she finds him too attractive to permit them to capture him again. Cross-armed and stony faced, Phoenix stands stoically as the ceiling begins to collapse around her. Ten minutes of falling debris, she tells "Fantomex". Run.
Standing over the corpse of Weapon XII, Xavier and his X-Men greet the arriving troops. Their commander, an old soldier in a command beret, tells Xavier that he recognizes him. He's seen him on TV, with the light whanging off his sweaty shaved head, just like it's doing now. Recalling Xavier's reported telepathy, he tells the professor that if he looks into this "dumb chimpanzee's head" he won't find anything except re-runs of the adult channel. Taking the offer as genuine, Xavier does so and then voices his surprise; he thought that the soldier was joking. Smiling broadly, the commander boasts that it's a little thing that they've been teaching them to protect the privacy of their minds.
The introductions over, the commander tells Xavier that the official story, if they want their activities to continue to meet the encouragement of the appropriate authorities, is that "the nice X-Men were on hand for a biological weapons accident in the Eurotunnel. Many lives were saved, but one fine mutant died a hero. Boo hoo. We love you." This statement/warning said, the commander tells the X-Men to stand aside, while they take back what's theirs and get this hole cleaned up. Moments later when the troops reach the derailed train, the troops find not their missing weapon, but Phoenix. Staring down the tunnel that leads toward the British Isle, she apologizes. She doesn't know what happened. He must have slipped by her. Weapon Thirteen, she says, has left the house.