Earth, in the year of our lord 3999 AD, where a man called Cable, aligned with rebel forces, battles the powers that be. But the struggle is not going his way at the moment. The muscular Cable dodges an energy blast fired by a large robot that skulks after him. Gunfire smoke pours out of Cable's weapon as he runs between ruined buildings in a ruined city. Cable glances back, he knows that they are in trouble, as Apocalypse's forces are routing them. 'We need time to re-group! Only one way to get that! Send this tin can to robot heaven!' Cable shouts as he fires a blast from his large weapon, which strikes the robot, exploding it into scrap metal. A woman with short dark hair wearing a blue costume similar to Cable's is positioned in a trench that Cable leaps into. Her name is Hope, and she tells him that they are so outnumbered, and that this is only delaying the inevitable. 'I don't want to hear the kind of talk, soldier! We fight until the last man – or woman – falls!' Cable calls back.
Hope turns to Cable and apologizes. 'It's just that so many of us have fallen already...' she utters, to which Cable tells her that all the more reason to fight on. He asks Hope if she wants those other rebel deaths to be for nothing. 'Of course not' Hope replies, tears in her eyes. 'Especially your brother's' Cable adds. 'No!' Hope exclaims. A man with cybernetic arms called Garrison Kane warns Cable that the enemy will swarm over them if they stay in this ditch. 'What should we do?' Hope asks. 'The last thing these walking tin cans will expect! A full frontal assault! Let's move out!' Cable shouts. The three rebels, along with a woman with long red hair known as Dawnsilk leap from the trench, 'For the rebellion!' Kane shouts. 'FORWAAARRRD!' Cable orders his teammates as they fire at the robots with their various weapons.
The robots begin to fall, torn apart by the rebels. 'It's incredible! They're going down!' Dawnsilk calls out. Cable tells the other rebels to keep varying their strategy and attack mode, and not to give the enemy time to adjust. He then orders them into formation alpha prime as Hope destroys one of the robots. 'Do a full sweep – short pulse bursts!' Cable tells the others as he takes out three of the robots at once. 'He's magnificent! No one else could have rallied us like this!' Hope thinks to herself, before asking Cable if they should try to take a prisoner. 'What for – they're robots! The only thing they can tell us is whether they dream of electric sheep!' Cable replies, before detecting something behind him – he turns around and discovers the ancient mutant known as Apocalypse! The diabolical villain stands on a human skull as buildings behind him burn. 'Vermin! How much longer can you ragtag rebels go on before I've eradicated you all?' he booms.
Apocalypse orders his machines to battle on, to move in epsilon formation, to surround the remaining rebels and destroy them. Suddenly, Apocalypse notices a whirlwind-like storm appear behind him. 'An incipient temporal storm!' he exclaims. The rebels see the storm as well, and Cable tells hope that the maelstrom is not the doing of Apocalypse, but if it is what he said it was, then its effects will be catastrophic. 'Prepare to back off!' Cable calls out – but it's too late, as the funnel sweeps towards Hope. 'I'm caught!' she calls out, unable to break free. 'No! Get back!' Cable exclaims, but Hope vanishes within the temporal storm. 'She's gone' Cable utters. The robots continue to close in on Cable, so he opens fire, and hopes that the other rebels have taken cover. Cable notices the temporal storm bearing down on him fast – he has no chance of escape, and us sucked into the storm – but one of the robots opens fire into the storm, and blasts Cable out of it.
Cable bounces along the ground, he can't understand why the robots aren't affected by the storm, and wonders if it is just organic material that is taken. Falling down the side of a cliff, Cable knows that he has to get some answers so he can deal with this, and calls out to his computer, asking it to assess the current situation and advise. The computer informs Cable that current time is being displaced by a temporal storm, and that the past is altering, with the Timestream realigning, meaning their present is reconfiguring to the existence of a new past. 'What must I do?' Cable asks, before ducking as one of the robots fires towards him, nearly striking him. 'Eat some plasma, junkpiles!' Cable shouts as he leaps up and opens fire. But Cable turns and runs into an old high rise building, deciding that fighting these droids is a useless exercise now until he has pinpointed the source of the anomalous chronal event – and he knows that everything they have fought for could be undone.
Taking cover, Cable asks his computer what he must do, to which the computer tells him that there is no effective action, and that once the Timestream has realigned, he and his world will no longer exist! Cable holds up the small cube that is the computer and looks at an image that the computer enhances. 'Description. Specify' Cable instructs the computer – the image is of the mutant known as Bishop, and the computer tells Cable 'It begins with a time-traveller from the 21st Century – a mutant named Bishop'.
'Mission accomplished, Forge! Senator Kelly's life back in the Twentieth Century was saved!' Bishop calls out, throwing his arms in the air as he materializes in Forge's base. But Forge looks at Bishop and asks him what he is talking about – as nothing has changed, the plague still rages. 'What plague? There was nothing when I left' Bishop replies. Forge taps at some keys and a monitor brings up images of people sick with the plague. 'Have you forgotten this horror? Look, sickness is everywhere. Millions are dying!' Forge declares. Bishop looks shocked and tells Forge that he doesn't understand – for after Senator Kelly survived the assassination attempt, he became president and dedicated his efforts to mutant rights. Forge tells Bishop that he thinks time travel has addled his mind, but that if what he says is true, then his memories would have adjusted to the new timeline. 'Unlike you, I have not been outside time. I only know what the record shows... a backlash of hatred – a plague virus genetically engineered and released' Forge declares, explaining that at first people sickened, but they lived – and then the first mutant victim appeared.
'Then it's all our fault! I never should've gone back! What else...' Bishop begins, before Forge explains that inside mutant victims, the plague mutated, accelerating, turning deadly – mutants were blamed, but they were innocent. Bishop asks if the X-Men couldn't stop it, to which Forge asks 'X-Men? What are the X-Men?' Bishop looks shocked and tells Forge that he has to get him back to there. Forge reports that the temporal coordinates are set to the time of the outbreaks of the plague. 'I will stop it!' Bishop announces as he puts the temporal transceiver around his arm. Forge powers up the grid, while Bishop readjusts the temporal transceiver so that it keeps him in the proper time period without being thrust back here. Forge reminds Bishop that he knows the risk, and that there are many possible futures – and they never know to which one their actions will lead. 'True. But one man's actions may yet shape the future' Bishop declares, before leaping into the time-travel pod and exclaiming that he is that man – again!
Bishop experiences a sense of “non-being” and then, the welcome solidity of a late Twentieth Century alley in Manhattan. He runs the back of his head as he lands on the ground in the alleyway. He picks up a newspaper that is strewn on the ground and looks at it, realizing that he may have arrived too late to prevent the catastrophe.
'A future of unrelieved misery too horrible to contemplate' Bishop utters, before dropping the newspaper, the headline of which reads “Mystery Plague Spread Throughout State”. Bishop tells himself 'No. That way lies madness' and leaps to his feet, declaring that he must try, that there are still those who can help, even at this late hour – there are still the X-Men!
At a large shopping mall outside Salem Centre, New York. Jubilee and Ororo Munroe a.k.a. Storm are in the mall, where Jubilee apologizes to Storm, explaining that she broke her CD player again. A man in a blue suit stands nearby, watching them. He looks at a watch on his wrist that has a small screen and tells himself that those are the two, and that this is a chance for the Friends of Humanity to expose more mutants to the world – his name is Graydon Creed! 'Like, I wish I could control my powers as well as you do' Jubilee adds. 'Someday, child' Storm smiles at the younger mutant. Jubilee heads off and tells Storm that she will go get her Walkman fixed, while Storm walks towards the bookstore and tells Jubilee that she will wait for her here. Creed looks at the monitor on his watch and brings up an image of Jubilee, he reads that she has plasma generating powers, and tells himself that he must be careful, smiling as he decides that they can definitely make the best of this encounter to further the cause.
Inside the electronics store, 'Not you again! Is this a hobby of yours, kid – wrecking things?' the store owner asks as he looks at Jubilee's Walkman. 'Will tou take a look at it? It can't be that badly screwed up!' Jubilee replies. The man scratches his head and asks 'Are you kidding me?' This player's charred inside. I don't know how long it'll take to fix it'. Jubilee grins and tells him that she has got time, and that she will wait. 'Blasted kids!' the man thinks to himself as he heads into the repair room. Jubilee picks up a portable game device in the store and starts playing it, 'Mortal Kombat! Excellent!' she thinks to herself, unaware that Graydon Creed is looking around the store, and follows the shop owner into the repair room. He looks around to make sure no one saw him, and while the shop owner busies himself fixing Jubilee's Walkman, Creed fires some sort of weapon at him, that releases a gas around him.
Moments later, the shop owner returns to the counter and hands Jubilee her CD player, telling her that it is fixed. 'Uh-huh. Like, what's the damage?' Jubilee asks, when suddenly, the shop owner utters that he feels dizzy, and sick, then slumps over on the counter. Jubilee leaps back from him, scared, when Creed appears and points at her, shouting: 'Look what she did! She's one of those horrible plague-carrying mutants!' 'Get her!' another exclaims. 'No! I -' Jubilee utters, before her powers suddenly go out of control, and a plasma blast causes a television nearby to explode. In the bookstore, Storm hears the commotion, while Creed moves closer to Jubilee and calls her a plague carrier. 'We've got you now!' he warns her, while Jubilee tells him that it is not her fault, and that she is just a kid. 'Mist! Come forth! Blind them in their hatred!' Storm exclaims as she approaches the mob gathering around Jubilee. Storm then flies in and snatches Jubilee from mob, assuring her that she has her, and that they must leave before the mist dissipates and return to the Mansion where they will be safe. 'We're not safe anywhere, Ororo! They hate us – everybody hates us! I'm so scared all the time! Why does it have to be like this?' Jubilee utters. Storm fires a blast of lightning at a window, breaking it so that she can fly herself and Jubilee through, while she tells Jubilee that if she knew the answer, she would be more than a mutant – she would be a seer.
One hour later, at Professor Xavier's School for Gifted Youngsters, Dr Hank McCoy a.k.a. the Beast finishes examining Jubilee, and reports that he has run every test in the medical manual, and that he would venture to say she needs to add some more leafy greens and whole grains to her somewhat dilapidated diet – but on the matter of viral infection, she is as clean as the proverbial whistle. 'That's a relief' Jubilee replies, before turning to Jean Grey, who is wearing a lab coat, and asking her why all those dorks were down on her. 'Scapegoats' Jean responds. She leads Jubilee out of the lab and uses her telekinesis to hang the lab coat up on a hook as she explains to Jubilee that they are looking for someone to blame – that they are frightened. 'And you – we – are convenient targets'. Jubilee asks if it is ever going to change, to which the Beast tells her not to despair, that scientific inquiry can dispel the hysteria gripping the country – the truth will out.
Later that night, at the city hospital, the Beast sneaks unseen into the pathology lab. He scours the darkness for anyone who may be in the lab, but finds it empty – and plans to find the truth about that disease. He locates a microscope, some petrie dishes and other accoutrements that he needs – and finds a file, where he finds the electronics store clerk's name. The Beast retrieves a slide smeared with a blood sample. He examines the slide under the microscope and sees that the virus – or viruses – are penetrating the cell wall of the tissue, linking with the chromosomes in the nucleus, resulting in an instant takeover. 'Curiouser and curiouser, as the celebrated blonde bimbo once exclaimed' the Beast thinks to himself, narrowing his eyes.
At that moment, in the X-Men's War Room, Scott Summers a.k.a. Cyclops and Jean Grey are watching a news report, where the reporter states that city officials have begun the quarantine in an effort to control the mysterious illness which is sweeping the country. 'This is unbelievable!' Scott exclaims, before turning as Storm flies into the room, along with Rogue, Logan a.k.a. Wolverine and Remy LeBeau a.k.a. Gambit. Scott informs them that he called them here to watch the news report. Rogue tells him that she hopes it was important, as she was getting ready to turn in. 'Spare us the sleeping habits, darlin'. I already don't like what I'm seein' on that screen' Logan exclaims, as they see footage of a mutant safe house in the city being sealed off by officials in an effort to prevent the spread of the virus by mutants. Gambit frowns, while Storm remains expressionless. Rogue clenches a fist and grits her teeth while Jean bites her lip. Cyclops looks thoughtful as Wolverine snarls and pops his claws. Footage shows a man in the crowd shouting 'Get rid of the mutants! It's the only way to stop the plague!' and Storm announces that she has seen that man, that he was at the mall – the one who attacked Jubilee. 'That's all I need to hear! X-Men... let's move out!' Cyclops exclaims.
At the mutant safe house, Bishop has arrived and watches as an angry crowd has gathered. 'It's the plague! Burn those stinkin' muties out!' one of the crowd shouts, while Bishop laments that it has already begun, but tells himself that there must be a way to quell the disturbance. He walks into the crowd and tells them to listen to him – that this plague is not caused by mutants, that they are mistaken. 'Hey, buddy! We're burning that building down if that's what it takes. Got a problem with that...brother?' one of the mob asks, as several of them hurl rocks and bottles towards the safehouse. One of the mob turns to Bishop and declare that he bets he is a lousy mutie – carrying the plague himself. 'Yeah, he's one of 'em! Nail him!' another of the crowd exclaims. But Bishop puts himself in danger, stepping between the crowd and the safehouse and tells them all to stop this, that he is spreading something as ugly as any plague – hatred!
Rogue and Storm appear overhead, and Rogue alerts Storm to Bishop as he continues to be hassled by the mob. 'Goddess! It's Bishop! Why is he here?' Storm wonders, before she radios Cyclops and reports that the mob has found a new taget in Bishop. In the Blackbird, Cyclops is with Jean, Wolverine and Gambit as he tells Storm that they read her. 'What dat homme doing here?' Gambit asks. 'Your guess is as good as mine, Gambit. And there's only one sure way to find out' Cyclops replies, before a panel on the floor of the Blackbird opens, '... and that's to drop in on him' Cyclops exclaims as the X-Men leap from the Blackbird, Wolverine drops straight down towards Bishop, claws at the ready, Cyclops and Gambit follow, lowering themselves to the ground on a rope, while Jean telekinetically lowers herself. Cyclops tells Wolverine to control himself, and that they don't want any innocent people hurt. 'Don't worry, Cyke – I'm wearing my best pair of kid gloves' Logan jokes. 'Who -' Bishop utters, looking up to see Wolverine falling towards him.
'Put away that pistol, pal! This little clambake don't need you escalating the festivities!' Logan tells Bishop, while Cyclops gets to work keeping the crowd at bay, he blasts optic energy at the ground, 'Stay back and you don't be hurt!' he warns them, while Storm, hovering above, shouts 'Rains – descend and wash the streets clean of the vermin below!' Rain begins to pour, causing one of the mob to pull out a gun and aim it at Storm, boasting that he is gonna drop her – as she is raining on their parade and he will put a stop to it. But before he can open fire, Rogue swoops down and grabs him, causing him to drop his gun as she pulls him into the air. 'C'mon with me, Shugah! Ah got just the place for a piece of garbage like you!' Rogue calls out as she throws him into a nearby dumpster. 'There yuh go, sweetcheeks! Hope yuh real happy with yuh own kind – rats and roaches!' Rogue jokes.
At that moment, Wolverine has landed on Bishop and pins him to the ground, while Cyclops and Gambit run towards him, 'Wolverine – don't! Let's find out why Bishop's here!' Cyclops exclaims. 'You heard the man, rookie! We thought we saw the last of you! So you better have a good reason fer showing up here again!' Wolverine warns Bishop. 'If you'll just let me explain' Bishop replies, getting to his feet as Wolverine removes himself. Cyclops then points at Bishop and tells him that he did it this time, that he helped turn this situation into a riot. Bishop stands his ground as he explains that he was trying to save lives – theirs and millions in his future. 'What? Ain't we been through this dance before? I don't know what's going on, but when you show up, it's trouble!' Wolverine snarls, shoving his claws towards Bishop, who steps back and tells the X-Men that he will explain everything at their headquarters – simply enough for even Logan to understand.
Later, in the War Room, the Beast has joined the other X-Men as they all look towards Bishop when Cyclops tells him that he has the floor. Bishop thanks Cyclops, and informs the X-Men that when he returned to his time after his visit here, Forge had never heard of the X-Men, and unlike when he left, a plague now ravaged his era. Bishop tells the X-Men that, in his future, it is as if they all never existed, that they must have died in the plague without achieving notoriety – mutants will receive the blame, but someone else cooked up this deadly virus in a laboratory. 'We must stop whoever's behind it before it's too late! This injustice must not be allowed to stand!' Bishop exclaims. The Beast reports that Bishop is correct, and states that the virus was genetically engineered, and while it doesn't appear to be lethal now, it is dangerously unstable. The Beast puts a disc into the computer, which brings up a slide of the virus as he tells the others that once the virus spreads to the merry mutant population and combines with mutant DNA, theoretically, it could become deadly – dastardly – for everyone. 'As I've oft been known to intone... dum da dum dummm' the Beast adds. Cyclops tells him that they get the picture, and announces that they will find out who is responsible – but until then, they need to calm the plague hysteria, before Storm suggests that perhaps, in this matter, President Kelly might be of assistance.
At the headquarters of the Friends of Humanity, in the peaceful Virginia countryside, where, behind the placid facade is a lab deep beenath the earth, occupied by the leader of the Friends of Humanity, Graydon Creed, and a scientist. The two of them watch a media report, in which an announcer state that a spokesman for President Kelly has revealed that noted mutant scientist, Hank McCoy, will take part in the Senate committee hearing on the public health emergency scheduled for tomorrow in Washington. Creed declares that this fits their plans perfectly, and turns to the scientist, telling him that the plague scheme has worked well – that the public demands action, and when they see that freak McCoy infected on television at the hearing tomorrow, everyone will be convinced that mutants are responsible for the diseases. The scientist states that the must act quickly, because in a few months, the infected humans will begin to recover. Creed starts to leave the lab, remarking that it is time for stage two – to begin the infection of mutants. The scientist tells Creed that he agrees, before Creed instructs him to prepare the vials for shipment to their agents. When Creed is gone from the lab, the scientist thinks to himself 'How fitting! A disease to cleanse the Earth of the plague – of mutants – and humans!' And as a strange energy glows around him, he laughs a deep, booming, wicked laugh....