It’s dark. Jean is out on the Xavier Institute’s grounds. She’s using her powers to locate Wolverine who’s isolated himself outside. He pops out above her on a tree branch. He explains to Jean he needs to be left alone. Jean protests, telling him a week’s been long enough. Wolverine tells her as long as Sabretooth is in the house; he’s not going in. Jean continues on, telling Logan that Creed was slowly making progress. Logan doesn’t want to hear it. He tells her that if he’s needed she knows where to find him. With that, he disappears. Jean’s left to her thoughts. She realizes now that he’s run into the woods, she doesn’t recognize his psionic imprint. It’s as if he’s changed mentally.
Elsewhere on the estate, Bishop and Xavier are having a discussion about the team‘s recent trip to the past. Bishop has been having nightmares, only they seem real, more like memories instead of dreams. He keeps seeing a world where humans are slaughtered and a different team of X-Men exists; a truly horrible place. He asks Charles if he thinks he’s crazy. The Professor thinks the problem may be stress. He admits that his psi-patterns have changed since they came back from Israel. He also goes on to say that maybe what Bishop sees is the future.
In Yonkers, New York, a young man named Dennis Hogan exits a subway car. He walks off the subway platform and down some steps onto a sidewalk. He’s hungry so he walks across the street to a small diner. He knows he’s taking a much-needed break. After all, he’s been traveling for the past few days, in search of Charles Xavier. He tries to calm himself before entering the eatery. He needs to stay calm in order to keep his mutant power under control. At this point his right hand takes on a scaly texture and he hides it in his pocket, while trying to calm down. Then he walks in.
Manhattan, at the CNBC cable news network studio, Trish Tilby is pacing around rather anxiously. She attempts to reassure herself that what she’s about to do is for the good of the people; she knows that she will be betraying a friend. A man walks in by the name of Clay and interrupts her. He wants to know if she’s continuing with the story, if she’s found someone to confirm the rumors. She tells him she does, a head researcher from Muir Island. Clay tries to convince her not to do it. He tells her the hatred of mutants will only increase if she goes ahead with the story. He asks her if she will be able to live with herself. In her hand she’s holding a brown folder. The label across the top reads “Legacy Virus”.
At the Belle Fourche River Dam, X-Factor is on the lookout for Mystique. There’s a Sentinel processing plant below the dam and word had it Mystique was going to blow the dam to flood it. Forge scales the dam wall and locates the bomb. Meanwhile below, Havok and Polaris help evacuate the workers. Val radios in to Forge and tells him she’s found Mystique. Forge tries to tell her to wait, but she pretends the transmission breaks up. Val goes after her alone. Mystique is running through a nearby cave. She knows she’s almost busted and pushes onward. A shadowy figure emerges and slices up her chest with his arm. The shape says, “It… begins” and disappears. Val finds her soon after and calls in a medivac. Forge thinks to himself about his troubled past with Mystique.
Back at Xavier’s Institute, Hank and Scott are fixing up some eats in the kitchen. They talk about Gambit’s comatose condition and how it’s affecting Storm and Rogue. They leave, food in hand, and bump into Bishop in the hallway. They invite him to join them for a meal and he politely refuses. Then, out of nowhere, he grabs Scott by the face, whips out his gun and points it at Hank. He calls them “butchers” and accuses them of crimes committed in the name of the “High Lord”. Cyclops uses his optic blast to disintegrate Bishop’s gun. This only angers him more and he absorbs part of Cyclops’s energy blast to re-channel and use it against him. He rears back to deck Scott. Cyclops tries to calm him down, but Bishop tells him he won’t listen to his “lies” anymore. Beast takes to the air and somersaults over Bishop’s head, kicking him in the face. Cyclops grabs Bishop and pushes him back. Then Bishop’s mood changes. He wants to know why Scott and Hank are attacking him. Scott tells him that he tried to kill them. Bishop, looking rather scared, wants to know what’s happening to him.
Back in Yonkers, Dennis is about to receive his soup. The waitress seems to have taken a liking to him and flirts a little. He thinks to himself he shouldn’t hook up with a human, and then gets angry with himself for thinking such a thing. He’s still a human. On the diner’s TV a news report about the Legacy Virus comes on. Dennis can feel his whole arm morphing. He needs to calm himself down and hopes that he will find the X-Men soon.
Inside a drainage pipe at the George Washington Bridge, a bum by the name of Jim Davis is about to meet his maker. He had followed a bright light emanating from this tunnel and it is this light that draws him further in. Suddenly, three bones spikes course through his body and come clean out his back. He falls dead. His attacker, Marrow, picks him up by the hair and drags him away from the ceremony of light, which she was performing. No humans allowed after all. Marrow remembers the last time the ceremony was performed decades ago. Some fellow mutants did it back then, although they were not part of the Morlocks. She goes on to say that something big is going to happen and it will happen soon.
Back at the mansion, Scott, Bishop and Hank continue their walk to Ororo. Bishop wants more tests done on him to see what’s wrong. Scott and Hank try to argue, but Bishop insists that it’s for the team’s safety. They reluctantly agree. Beast opens the door to Gambit’s med-room and sees Storm sitting next to the comatose Cajun. They drop off her food and leave to run those tests on Bishop. Storm is left to wonder what’s going on. Then she wonders why he and Rogue had to kiss in the first place and what caused Rogue to leave so abruptly. She asks aloud what secret Gambit could have that would scare Rogue off.
Speaking of Rogue, her and Iceman’s are currently in Key Largo, Florida. They’re at a nightclub and Rogue is beboppin’ with some dude on the dance floor. The guy tries to grab Rogue’s bare arm, so Bobby comes over and attempts to keep him away. The big galoot grabs Bobby by the shoulder. Then he slips on a patch of ice that suddenly appeared on the floor. Most of the dancers turn to look at what’s going on. Not Bobby though. Something else has caught his attention. On a nearby TV a breaking news report has just been announced. Trish Tilby is breaking the news on the Legacy Virus.
At Xavier’s School for Gifted Youngsters, the newest generation of mutant superheroes are plopped down in front of the boob tube. They too are watching the news report and are none too happy. Tilby goes on to report that at least one human has been affected by the supposed mutant disease. Jubilee calls for Banshee and the White Queen to check it out.
In Washington D.C., Senator Robert Kelly also sees the news. At the mention of Multiple Man’s death and X-Factor’s involvement he becomes angry. He gets on the phone and demands to be connected to Forge and Val Cooper.
Moira MacTaggert and Rory Campbell are also present on Muir Island to hear Ms. Tilby’s report. Trish continues her report saying Moira was the lone human so far that is infected by the virus. Moira shuts off the TV. Rory wants to know what they should do. Moira tells him she doesn’t know.
Back at the diner, the people watching the newscast are upset. They start spewing anti-mutant propaganda. Dennis pays his bill and silently leaves the restaurant. The patrons continue with mutant jokes until one of them notices the door still open. They suspect that Dennis left in a hurry because he might have been a mutant, or worse, an infected mutant. They aim to find out.
At the mansion, the X-Men watch as Trish’s report finishes. The most affected person in the room is Hank, who happens to have a relationship with Trish. Everyone tries to comfort him, but he remains upset. He storms off. The X-Men discuss what the next course of action should be. Professor X tells Scott to contact Cable; he has an offer for him. Suddenly the Professor and Psylocke reel back in pain. A powerful psionic presence just fell to Earth and the backlash was tremendous.
Indeed, somewhere in Switzerland, a fiery comet falls from the sky. From afar, a being called Blaquesmith watches on his data screen. He tells the computer to lock onto the coordinates. A close-up of the landing site shows that it wasn’t a comet, but a man. Nate Grey, aka X-Man, has crossed over from the Age of Apocalypse. Blaquesmith notes to himself that this is not the first temporal rift he witnesses.
Somewhere in England, a mutant by the name of Emplate shows up at the Edgerton estate. He wants to see Lady Gayle and he won’t take no for an answer. Niles, the butler, shows him the way. Niles brings Emplate to Gayle’s room. Gayle’s inside sitting in a wheelchair stoking the fire. Emplate moves in to talk and receives a hot poker in the chest. He starts to laugh for it doesn’t hurt him. He wants to know more about Jonothon Starsmore and he knows Gayle has some answers.
Back in New York, Dennis is running through the back streets of Yonkers. He trips over his own feet and falls to the ground. Dennis wonders if he should just give up. He knows the kids from the diner are chasing him, but he just wants to be left alone. He decides to get up and hopes that the rumors of the Xavier Institute being connected to the X-Men are true. Right away headlights shine on him. The kids have caught up. They accuse him of being a mutant, shaking the weapons in their hands. He pleads with them, but it’s no use. They move in for a beat down. Dennis suddenly morphs all the way and turns green and scaly. He’s nowhere near calm and can no longer control his mutation. A girl gets scared and yells for help. One of the guys takes a bat to Dennis’ head. Then, as he lay there, they proceeded to beat the life out of him.
Just then at the mansion, Xavier telepathically receives Dennis’ fears and pain. He tells Storm they need to head north immediately. She hurls him up with her winds and they take off. He reaches out to his X-Men with his mind and asks for his assistance.
In Murderworld, current home of X-Force, Cable interrupts the team’s practice session. He seems pretty irate. Up in the control deck, a hologram of Arcade’s head appears to Domino. Arcade has detected them in his hideout and has set the place to self-destruct. He tells her they have a minute to evacuate. They all make it out of there even though the place blew up after only 50 seconds. Warpath went back in to get Sunspot, and Siryn wonders if that is wise, considering all that Sunspot has done while he was Reignfire. However as the dust settles, they see Sunspot carrying Warpath out of the rubble. He says that thanks to Cable he is free of the Reignfire persona and ready to take his place among the team again. X-Force are surprised to see Cyclops standing there. He tells Cable that Xavier wants to have a word with them. Cable, of course, is happy to oblige.
Back in Wyoming, X-Factor is still dealing with the Mystique situation. Havok and Polaris are making sure the area is evacuated while Forge tends to the shapeshifter’s safety. He runs over to her location and only sees Val, lying on the ground. She says that Mystique only played possum and got away, and then asks Forge to help her get up. Forge knows that the real Val would never do that and kicks her in the face. “Val“ falls back unconscious and reverts back to her true form, Mystique. The real Val comes out from the cave. She makes a comment about their future plans for Mystique and how she probably won’t like them. Forge radios Polaris to see if they’re ready to go. She gives him the affirmative and just then Havok starts pulsating with energy. Then the dam explodes. Val yells at Forge about disarming the bomb. He assures her he did and that there must have been another one. Polaris comes flying over with Havok in her arms. They’re all right, but it wasn’t a bomb that went off, it was Havok !
In Hammer Bay, the capital of Genosha, Kitty Pryde, Douglock, Pete Wisdom and Mr. Edgerton, Genosha’s oldest mutate, search for evidence of the weapon being used to kill the mutates. Edgerton is looking through some papers of Dr. Moreau and is frightened by what he reads. He mentions something about the end of the world. Wisdom tells them to hurry it up. They need to meet up with Captain Britain and Nightcrawler. Somewhere else, Sugar Man is sitting at his desk watching the foursome as they search for their clues. He’s afraid they’re getting too close. So he incinerates mutate number 01. Not only is Mr. Edgerton destroyed, but the papers he was holding as well. Sugar Man definitely does not want to be found, he managed to stay hidden ever since he arrived in the timeline twenty years ago.
At Avalon up in space, Colossus and a trio of his fellow Acolytes head outside to examine something floating near the station. Milan links up with Exodus, who’s inside, so he can watch what’s going on. Exodus orders Colossus to bring the object inside. Then he goes on to tell the other Acolytes that it might be a sign. Amelia Voght thinks to herself that Exodus might be wrong to bring this thing on board. After all, they don’t know what it is. Outside, the team reaches the object. It’s actually a huge ball of ice. Piotr orders Rusty to melt it down with his powers though It flares up itself from within and everyone backs off. Now that most of it is melted away they can see there’s a person inside and that this person is alive.
In the sewer tunnels, Marrow has finished the Ceremony of Light, though without the desired effect – her fellows did not come. Someone extinguishes the candle flame and the lights disappear. She turns to see whom it is and is happy to see it is her “father”, the one who made them. She wasn’t sure if she would ever see him. She tells him she’s is one of many others who are finally tired of hiding what they are. He reaches out his hand and comforts her. It’s the Dark Beast who has also made it to the main reality. He can tell she’s a descendant of a Morlock. After all, they were his work. McCoy mentions that most of the Morlocks turned out to be a disappointment, besides Callisto of course. He then asks Marrow how many more like her there are, and she replies that six of them are ready to wreak havoc on the humans. Dark McCoy smiles.
Back in New York, the kids are still beating on Dennis while Professor and Storm fly to the rescue. Dennis takes a few more blows and the Professor goes blank. His mind goes out to Dennis to be with him during his torment. He can feel every punch and every kick. He can hear what they’re saying, but can’t really see them because of all the blood. Then the bat comes down on Dennis again and the Professor feels nothing. He’s ripped from Dennis’ body and screams in despair. He knows it’s too late. They won’t make it on time. The teenagers stop knowing the mutant is dead. They run off without a care that they murdered someone. They only saw Dennis as a mutant, not a person.
Wolverine, Bishop, Archangel, Psylocke, Storm and Jean arrive at Dennis’ body shortly after. Charles’ astral form reenters his own body being carried by Warren. The Professor calls out to Dennis and, surprisingly, he answers. He whispers that he knew the X-Men would help him. Charles tells him to rest. The boy is dead. The professor goes on to tell his X-Men they need to fight for a better world or else this is what the future holds for them.