Standing in a snowstorm in the mountains of Afghanistan, Wolverine stands over a dozen dead soldiers, all of whom he has just killed. His bloodstained claws still unsheathed, Wolverine snarls at the only soldier still alive. Eyeing the Rapmund 429 pistol the young man is holding, Wolverine asks him what does it take to get them to listen to reason? Here he is, trying his best to honor the strict pacifist principles of the Xavier Institute, and here is a bunch of slave traders, filling him full of lead. Informing the young man that he can’t kill him, Wolverine tells him that if he gets stung by one more stupid bullet, he’s going to lose his hand, okay? Drop the gun, Wolverine tells him. After the soldier drops his weapon, Wolverine turns his back, calling him a wise man. As Wolverine walks away, he tells the soldier to tell the reinforcements he called to turn back. He’s feeling mean.
As the X-Man is leaving, the soldier picks his pistol back up and fires. The bullet grazes Wolverine’s jaw, as he turns at the sound of the gunshot. In a flash as swift as the wind, the soldier’s gun, as well as the hand attached to it, separates from the soldier’s body, falling to the ground. Looming over the shocked soldier, Wolverine shows his claws and asks him what was he thinking? “That guy doesn’t look like a deranged human killing machine with a hair trigger fuse?” Stammering and unable to form a single word, the soldier sits in near silence as Wolverine turns to leave again. Walking away, he tells the soldier to quit while he can still hold hands with his sweetheart.
Standing on a hill, Wolverine views the simple encampment, now in flames, that was once the headquarters of the slavers. Sniffing something in the air, Wolverine strolls down the hill to the compound. Entering one of the tents, the X-Man finds the decomposed remains of half a dozen people. Standing among the corpses and holding an unconscious woman clad in a burka, Wolverine finds a man, clad in a white trench coat with a costume and cowl to watch. Asked by Wolverine if he knows him, the man introduces himself as Fantomex, Europe’s most wanted super-thief, who is thieving as usual. Informing the X-Man that his Professor X and Miss Jean Grey ran into him recently on their way east, Fantomex suggests that perhaps it is they whom he smells on him.
After placing the woman upon the ground, Fantomex holds up a ledger to Wolverine, telling him that it contains the names and addresses of some of the richest people on the planet. The trade in mutant slaves, he informs Wolverine, joins the lowest with the highest. Can he imagine, he asks, what they’ll pay to keep their names out of the press? Horrified at Fantomex’s statement, Wolverine replies in surprise that he can think about money while women and kids are treated like furniture. Unapologetic, Fantomex retorts that he is only human. He is nothing like Wolverine’s “X-Men”.
Placing the ledger in an inside pocket of his coat, Fantomex wonders aloud to Wolverine how much money he would pay to learn the secrets of the Weapon Plus program… and his own lost past. As Weapon X, Fantomex tells Wolverine, he spent the best years of his life being tortured in the project laboratories, did he not… James?
Confused at the name, Wolverine asks Fantomex what he is talking about. Finally recalling the name, Wolverine tells Fantomex he is Weapon Thirteen, Ex-One-One-One, the latest state-of-the-art supersoldier, right? Replying evasively, Fantomex tells Wolverine that he will be hearing a lot more about that soon enough. In the meantime, Fantomex says, changing the subject, he didn’t kill these slave traders. Pointing to the still unconscious burka-clad woman, Fantomex tells Wolverine that the girl did. They tried to remove her burka and… something happened. The flesh was stripped from their bones.
Raising his arms, Fantomex quickly becomes engulfed in a concealing mist. Disappearing from sight, he informs Wolverine that he counts thirteen armed and inquisitive mercenaries heading this way. To this, he tells the X-Man he is sure he can talk some sense into them. As the mercenaries enter through the tent’s flap, Wolverine pops his claws and mockingly tells the departed Fantomex that he bets.
Several thousand feet above the surface of the Earth, a man on flight 1212 of Air India brandishes his pistol while holding tightly a woman he has taken hostage. Addressing the whole airplane, he tells them that in the name of the liberation of Kashmir, this aircraft is now a weapon in a righteous cause! Along with his two accomplices, the gunman makes his way to the cockpit of the aircraft. Mocking airport security, their x-rays and passports, he tells the passengers to stay in their seats and the captain to turn towards New Delhi. As he makes his way toward the cockpit, the gunman hears a voice of a man excusing himself. Turning to the man who has spoken, the gunman sees a middle-aged, bald man, sitting next to a young flame-red haired woman. Utterly calm in demeanor, the man rhetorically asks the gunman if those are wax guns, aren’t they?
Still holding the pistol to his hostage’s head, the gunman informs the passenger that he will kill the woman and then he will kill him. As the red-haired woman next to him returns to her book, the bald man tells the gunman that he will not. Now pointing the pistol at the passenger, the gunman tells him to shut up. Suddenly realizing something, the hijacker stammers the recognition that the passenger is speaking Pakistani. The rage subsiding in his demeanor, the would-be hijacker asks the man weakly what should they do instead?
His blue eyes transfixed on the gunman, peering into his mind as much as examining his features, the bald man suggests to all the gunmen if it wouldn’t be much better for everyone if they all turned around and walked back to their seats. They could just stay there until they land in Mumbai. As the former hijackers return to their seats as instructed, the man suggests to one of them, Mohammed, that disarming the bomb in his bowel might be a good idea too. Jean, he informs the man, could do that for him. She’s a telekinetic.
The crisis averted, the bald man turns to Jean and tells her that he’d just been reading about these so-called “dirty bombs”… To the rest of the silent passengers’ surprise, the three former-hijackers return to their seats and buckle themselves back in. Back at his own seat, the bald man picks back up the French news magazine he was reading moments ago. The cover of the magazine sports the man’s image, next to a caption identifying him as “Le Professeur X”. Returning his attention to the magazine, the Professor tells Jean that the world seems to get more dangerous every day.
At the Mumbai Airport, a crowd gathers around the bottom of the staircase, where the disembarking passengers are descending. Among them are a dozen Indian law-enforcement officials. Descending the staircase, Xavier is flanked by the former hijacker who had accosted him earlier. The gunman and his two accomplices, have their hands clasped behind their head in the surrender position. His arm on the former gunman’s shoulder, Xavier introduces him as Mohammed to the crowd below. He tells them that an hour ago, Mohammed was convinced that territorial injustices allegedly perpetrated by one tribe against another justified turning an aircraft into an atomic weapon and killing thousands of innocent people. They, Xavier continues, have had a talk since then…
After Xavier informs the crowd that he explained some of the destructive inconsistencies and contradictions in Mohammed’s thinking, Mohammed tearfully agrees. He tells the crowd that he doesn’t know what he’s been doing with his life. Taking the three hijackers into custody, the head official thanks Xavier, telling him that they are in his debt. Addressing the official by his name, Tajinder, Xavier informs him that he is a telepath and he can absolutely assure him that none of the men will never again use violence in the service of abstract ideas. Just as, Xavier continues, staring intently on Tajinder’s eyes, that he can assure them that they will not be brutalized in his custody.
Hearing someone calling out to him, the Professor turns to see the approaching Proudstar, Feral and Thornn, running at full speed. As Proudstar yells to the Professor to look out, far away, an unseen gunman centers Xavier in his rifle’s scope. Calling Xavier a monster, the sniper commands that he die, and squeezes the trigger. As the deadly projectile whizzes past her, Phoenix, already using her powers to sense the intricate world around her, telekinetically grabs it with a mentally constructed talon of fire.
Still scant moments from the warning, Xavier scarcely begins to grasp what his former student has done before being tackled to the ground by Proudstar. Identifying James Proudstar with surprise, the Professor informs him that he thought he was dead. Replying with a bit of dry humor, Proudstar retorts that it must have been someone else. Pointing a nearby building, Proudstar asks the rest if they can hear the breathing?
Examining the projectile from her mental fire-talon, Phoenix informs the Professor that it is not an ordinary bullet. Telling him to look at it, she tells him that she doesn’t even think it’s from this planet. It has a really weird molecular ringtone. More interested in immediate action than questions, Proudstar, Feral and Thornn leap through the window into the room of the sniper. Grabbing the sniper, completely covered in a hood and robes, Feral tells the others to help her, so they can see who’s underneath. Examining the sniper’s weapon, Thornn calls Feral a treacherous cow and tells her to help herself. Asking his teammates please, to have some dignity, Proudstar removes the hood, revealing Shi’ar Empress Lilandra, adorned in her battle armor. Her eyes red with rage, Lilandra struggles against her captors and screams the name of Cassandra.
Having left the airport on foot, Professor Xavier stands in horror. Looking on in dumbfounding shock, he realizes that his would-be assassin is Lilandra. Worse, she thinks he is Cassandra Nova. Trying to get the Professor’s attention, Phoenix points out an approaching car that, she says, has exactly the same molecular tone from the bullet. It’s not from here, she tells him. Still concentrating on the revelation of Lilandra, the Professor examines her unconscious form, which Proudstar holds in his arms.
Still holding the Professor’s ex-lover, Proudstar apologizes about this introduction to the Mumbai branch of the worldwide X-Corporation. They were going to all dress in their new costumes and sing the national anthem for a laugh. Handing Lilandra over to the Professor, he tells him that he thinks she is an alien and then asks him if he has any idea why she would want to assassinate him? Cradling Lilandra’s head in his hands, the Professor tells Proudstar that her mind is sick. She thought he was someone else… someone who hurt her badly. His face contorted in grief, Xavier asks her to forgive him. Standing in the back of the group, confused, Thornn asks the rest who the woman is. She missed that bit. Responding snidely, Feral calls her stupid and asks if she doesn’t read? She’s a space empress.
Stepping from the car that Phoenix had been studying moments before, three elderly men with beards, all exact in appearance, call to the Professor. Informing Xavier that the heavens are in turmoil, they tell him he must come with them. Judgment, one tells him, must fall on the planet Earth. Turning to the members of the Mumbai X-Corporation, Xavier informs them, with halting speech, that Lilandra is a woman from another world. She is his wife and consort. Jean, he tells them, will explain. Referring to the now four doppelgangers, Xavier tells the group that he’d better go with them.
Deep in the Mumbai X-Corp HQ, Wolverine sleeps soundly. Regarding the snoring X-Man, Sunfire tells the rest of the team that he was there when he returned from his mission in Russia and couldn’t be waked. Laying her jacket on a chair, Phoenix tells Sunfire that he’d better just leave him. He does that, she informs the group. His healing factor takes a lot out of him. Eyeing the sleeping man, Thornn asks the rest if it is indeed Wolverine. Sarcastically, Feral replies that one can tell by the stink of his jacket.
Looking around the room, Phoenix asks if Wolverine wasn’t supposed to have someone with him. Replying that he did, Thornn informs Phoenix that Wolverine left a message to say he was on the Afghanistan/Pakistan border rescuing some mutant refugee, but they had all headed out to meet her and the Professor. Changing the subject abruptly, Thornn points out that the Professor’s wife is a pretty good shot.
Blowing dust off of a Cerebra helmet, Feral apologizes for the place, calling it a disgusting mess. She tells Phoenix that she would clean it herself, but it seems so demeaning for a so-called super hero. Lowering her voice to a whisper, she adds that the Hindu Times called her a super hero last week. As Phoenix steps into the Cerebra chamber, preparing to don the matching helmet, Thornn comments to her that it is weird how they really love their old outfits here. Asia, she tells her, goes crazy for all the tight, spangly Bollywood costumes everybody else hates.
After replying that she noticed, Phoenix asks Feral what exactly she said was wrong with their Cerebra link? Shrugging her shoulders in frustration, Feral remarks that the main problem is that they have no telepaths worth half a damn in the X-Corporation Mumbai. That’s the bottom line. Asking her to take a look at them, Thornn tells Phoenix that they can’t even figure out the controls for the DVD! What chance do they have of starting up a sci-fi machine? Donning the Cerebra helmet, Phoenix tells Thornn her point is taken. It’s not all that difficult, she tells them, you just think into it and it finds mutants for you. Telepathically activating the machine, Phoenix tells the two that maybe she can kick-start their Cerebra… and track down the missing mutant.
As Phoenix begins her search, the rest of the group begins theirs, combing the X-Corp building. Remarking to the immobile Sunfire, his hands planted squarely on his hips, Feral tells him to not just stand there and tell everyone he’s using his special nuclear powers to do all the work. Sounding a little hurt, Sunfire begins to defend himself, informing her that he is using his special nuclear powers… Proudstar, receiving an update from the HQ’s sensors, informs the rest that the place is scanning free of all intruders. Digesting this information, Thornn remarks that the mystery mutant could be anywhere by now. If she even exists. Examining the still slumbering Wolverine, Feral suggests perhaps he ate her for lunch. Suddenly making a startling revelation, Feral informs the group that it is he! All of this dust, she tells the group, is coming off of Wolverine.
As the group gathers around the unconscious X-Man, Proudstar warns Feral to not touch him! Wolverine might wake up and kill her! Trying to warn Feral as well of her actions, Sunfire asks her if she is insane? He’s a samurai! Samurai? Feral asks. But he was on a search and rescue mission, she asks. Who did he rescue?
Smiling from beneath the Cerebra helmet, Phoenix sounds a triumphant “gotcha.” The missing mutant, she tells the group, is right there in the room with them after all. Asking Phoenix, who is emerging from the Cerebra chamber, if she is sure, Proudstar tells her that his senses are working overtime and there’s still only six of them there. Examining the dust, which covers sections of the floor, Phoenix tells the Proudstar that she’s not strictly biological right now. Are you, she asks the dust?
Crouching down and playing with her hair as she smiles, Phoenix tells Sooraya hello. It’s okay, she tells the dust. She is Jean. Jean Grey-Summers, and she is safe there. As the dust begins to rise into the air of its own accord, Phoenix tells it that they are the X-Men. They got her out of the camp. She is safe. As the dust now begins to coalesce into a single, cloudy mass, Phoenix tells her that she knows she is hungry. She can now turn back to human form now.
From among the dust cloud, bones begin to form, which quickly connect into a skeleton. Finishing the transformation, the skeleton becomes a woman, dressed from head to toe in a black burka, leaving only her green eyes visible. Speaking only a single word, she mutters “Turaab,” followed by a more emphatic “Turaab!” Not moving an inch in his nearby bunk, the now-conscious Wolverine informs the rest that it means “dust.” It, he tells them, is all she says. Now will everybody shut up? He’s trying to sleep. Saying hi, Phoenix tells Sooraya it’s okay. They’re friends. Everything’s going to be okay.
From behind the wheel of the Earth vehicle called a “car,” an elderly Shi’ar man, no longer disguised as human, tells Professor Xavier that they are there. It is time to say goodbye. The Empress Lilandra, he tells him, must be returned to her people. A little confused, Xavier asks Araki what’s going to happen here? After pointing out that he is Araki 6, the elderly Shi’ar adds that he’s only a messenger of the Empire.
Emerging from the vehicle, Araki regards the giant Shi’ar vessel, which has landed before them, and the Institute students emerging from it. Informing Xavier that they are returning his people to him, Araki adds that, for their own protection during this time, the Empire can afford no further contact with the mutant race. Stammering slightly, Xavier asks Lilandra what is happening. Looking deeply into the eyes of her former consort, with eyes that once again reflect sanity, Lilandra tells Xavier that he thinks he knows everything. He thinks it can all be set right with words and hopes. His words bordering on desperation, Xavier tells Lilandra that Cassandra Nova can do no more harm. He knows what she did disguised as he, but… her mind will heal… the Empire will prevail.
Averting her eyes as they hold each other’s hands, Lilandra tells Xavier that, through him, ruin came to them. Always, he brings ruin. The Empire is broken, she says. She is broken. How can she allow them to see her like this? Not broken, Xavier replies to his love. Dissolved. Changed to a new form…
Purposefully interrupting Lilandra and Xavier’s personal moment, Araki 6 informs his empress that the new emergency senate has decreed the withdrawal of all Shi’Ar citizens from planet Earth during the disinfection period. Breaking away from Xavier’s embrace, Lilandra tells him that he doesn’t know anything. It’s over. Gazing at Xavier with harsh eyes, Araki tells him that the mutant species has registered toxic levels of aggression. Nature itself, Araki tells Xavier, has chosen to deal with his kind. His marriage to Empress Lilandra is hereby nullified.
As Araki leads the tear-filled Lilandra into the space ship, Xavier, finally considering Araki’s choice of words moments ago, asks what he meant by disinfection. Not looking back, Araki reaffirms his use of the word. The Phoenix has hatched, he informs the Professor. And she is merciless.