Robert Kelly, a senator from Massachusetts, stands in front of the Lincoln Memorial in Washington D.C. and addresses the nation. He is running for president of the United States in the first national election of the new millennium. Election is only a few short days away and, currently, he has a decent shot at winning an extremely close race. Kelly speaks at a podium ordained with roses and the emblem of the United States at the steps of the Lincoln Memorial, while Secret Service agents work in the background to ensure his safety. Filling up the streets in front of the memorial are Kelly’s supporters, all eager to hear what the candidate is going to say about one of the most decisive elections ever.
Kelly starts his speech and tells the people that he stands in the shadow of a man who once said, “a house divided against itself cannot stand.” He is in the shadow of a man who gave up his life to preserve the union and its hopes and ideals for which it stands. As back then with Lincoln, the world today is facing a clear and present danger. For Abraham Lincoln the threat was slavery. “For us,” says Kelly eloquently, “on this cusp of the 21st century, it is mutants!”
On Genosha, the master of magnetism known as Magneto watches the live coverage of Kelly giving his speech. His helmet is off and on a table while he paces the room with his hands behind his back. Kelly explains to the people that mutants are beings born with genetic “quirks,” which grant them capabilities that are far greater than humanity at large. Humans are Homo sapiens, while mutants have named themselves Homo sapiens superior.
Magneto thinks to himself that it is rightfully so of mutants to call themselves superior. Humanity has reached the end of its evolutionary road. Magneto relates humanity to the extinct dodo and how humans do not even realize it yet. He has dedicated his life to ascend mutantkind to where it should. Magneto tells Kelly that the politician will find Magneto a man of his word and anyone who opposes him will pay a fearful price.
On Muir Isle, Moira MacTaggart watches the new coverage on Kelly. As she and her fellow researchers continue their work, Moira listens as Kelly says that mutants are supposedly the next step in human evolution, which others believe that they are a different species all together, just as their Cro-Magnon ancestors were to the Neanderthals. Moira is disgusted by this remark and mutters to herself that they are all human, biologically speaking.
In San Francisco, the renegade mutant team known as X-Force watches the speech from their base. Pete Wisdom, Cannonball and Jesse Aaronson watch as Kelly states that some of the mutants have been called heroes. Angrily, Meltdown throws her book at the television and asks Kelly how many times those heroes have saved his life and the world. Proudstar tells Meltdown that she is wasting her breath and to save it for someone who cares. Nothing will change Kelly’s mind; he will hate mutants until he dies.
At the Massachusetts Academy, home of the students known as Generation X, Kelly announces that many mutants are properly condemned as terrorists. Chamber, Husk, Skin and M watch the report while Jubilee turns away in disgust. She tells her friends that if he were speaking about Blacks, Asians or Jews, people would spit in his eye. Jubilee wonders what makes them so awful that people hate them that much.
At the home of the X-Men, the Xavier Institute, the entire team gathers in front of the television to watch the speech. Beast sits by the television, while the Professor is behind him in his wheelchair, concentrating on the speech. Phoenix calms down the angry Nightcrawler on the couch next to the Professor. Wolverine leans against the wall with his arms folded in front of his chest, not saying a word. Cable, Psylocke, Storm and Colossus stand behind the couch, while Thunderbird comes down the stairs to join the rest of them. Gambit, Bishop and Rogue are to the side. Rogue sits on the floor by herself and is covered head to toe with her old Brotherhood uniform. She stares at the ground and listens as Bishop asks the others how Senator Kelly, a decent man, is able to say such things.
Beast tells his comrades that the scary part is that everything Kelly is saying makes perfect sense. The troubling question, though, is what Kelly plans on doing about it. Rogue tells Beast that, whatever it is, it will probably be bad. Beast tells the young girl that he refuses to believe that and he chooses to embrace hope. “More fool, you,” says Rogue.
In Glasgow, Scotland, a woman in a hotel room watches Kelly’s speech as he tells the people that mutants are a clear and present danger that not only threaten America, but the whole world. The woman loads her gun and shoots the television set. Mystique reloads her gun and tells Kelly that he does not know the half of it. The last time he ran for president, she did her best to try and kill him. However, she is determined as she is patient. Sinisterly, Mystique tells Kelly that if he plans on starting a war between humanity and mutantkind, then he should expect to be one of the first casualties.
Sometime later in the North Atlantic Ocean, the motor yacht called the Divinity cruises off the coast of Scotland. All seems peaceful until a helicopter pilot emerges from below deck and falls to his knees. He throws up and frantically screams to himself that everyone is sick and is going to die. He runs towards the helicopter, holding his stomach the whole time and tells himself that he can fly home and get some help, which will make him a hero. As he reaches the helicopter, a man with sharp nails and fangs from within the chopper tells him that he won’t be doing that in this lifetime. He then pulls the pilot in and kills him.
Sabretooth goes down below deck with Toad and introduces them to the Hellfire Club members below deck, all dressed in old European clothing. Sabretooth threatens to kill any of the terrified people if they even look at them cross-eyed. Toad tells Sabretooth that he is not impressed with how the other half live. Sabretooth tells his comrade that, once you kill one billionaire, you’ve killed them all. However, judging by the stench, they would be putting them out of their misery.
Sir Gordon Phillips, Lord Imperial of the Hellfire Club, leaves his wife’s side and approaches Sabretooth, demanding the meaning of the intrusion. Sabretooth tells Gordon that he may be powerful in his circle of friends, but that makes no difference to him. He then grabs Gordon’s wife and kisses her on the lips in front of the billionaire. Outraged, Gordon tells Sabretooth to let go of his wife, but Sabretooth grabs the man by the neck and cuts him off. Sabretooth tells Gordon that he gets points for having the guts to confront him, but tells the man not to push his like. “’Sides,” says Sabretooth, “This ain’t your wife.”
Lady Phillips looks at her husband and then suddenly shape shifts back into Mystique, who offers Lord Phillips her condolences, because before the departure the real Lady Phillips suffered a “regrettable and fatal accident.” Mystique ignores the horrified remarks of the angry Lord Phillips and walks over to the dying body of a man, who is being watched over by two terrified women. Mystique tells everyone that they have been given the privilege to be the lab rats for an experiment that will usher in a new era of peace for the world. The voyage was actually a test for the latest strand of the Legacy Virus, which has been modified to affect only humans, not mutants. Mystique turns to Lord Phillips, who is still being held by Sabretooth, and congratulates him on not having any symptoms of the disease. He is a mutant.
Spitefully, Lord Phillips tells Mystique that, if that makes him like her, then he would rather by dead. “Suit yourself,” says Mystique. Sabretooth snaps Lord Gordon’s neck. Mystique readdresses the rest of the passengers and tells them to consider this a culling of the human herd of all evolutionary “deadwood.” She knows this seems arbitrary and unfair, but fate is like that sometimes. For the greater good of some, it is necessary sacrifice a few. As Mystique, Sabretooth and Toad board the helicopter and fly away, Mystique hopes that the Hellfire Club will understand. Once the helicopter is safely away, the yacht explodes, killing all left onboard.
In the Danger Room, Gambit’s team of X-Men trains to hone their abilities, particularly the powers of their newest member, Bishop. Their opponents are the Sentinels. Phoenix is floating high above the battle, most likely with the help of Storm’s winds, with her eyes closed and linking all her teammates together with her telepathy so that each X-Man is aware of their comrade’s situation. Below, Gambit uses his charged playing cards to destroy the Sentinels, while above Storm attacks with raw lightning. Beast leaps atop a Sentinel’s head and rips out some circuitry, which Cable uses his telekinesis against a Sentinel which has him in its grip. Bishop takes in all the blasts of the Sentinels and channels the energy back to his opponents in a lethal force. Bishop destroys a Sentinel and tells his companions that they have the robots on the run.
A Sentinel falls to the ground and on its back is Fitzroy, alive and well, who criticizes Bishop for always thinking that he has won when the battle is still up in the air. Bishop is shocked and tells Fitzroy that he saw him die. Fitzroy laughs and tells Bishop that he is the Chronomancer and time is his domain to command. He asks Bishop that, where he is concerned, how can truly be what it seems. He then asks Bishop how it feels to know that he, Fitzroy, killed Shard and Bishop’s friends, and got away with it.
Bishop leaves the side of the X-Men and, in an angry rage, rushes towards Fitzroy. Fitzroy asks the man how he plans on stopping him and Bishop tells him that he will do it any way he has to. The Sentinels take advantage of the opening Bishop left and blast Cable against a wall. The Sentinels use their metal tentacles to wrap up Storm, who calls out to Bishop. Bishop either does not hear or chooses to ignore Storm, for he has gotten to Fitzroy and tells the man that he won’t get away this time. Fitzroy laughs and Bishop asks him what’s so funny. Fitzroy asks Bishop what price is revenge when it lets his friends get killed. Bishop follows Fitzroy’s gaze and sees his teammates, all dead and wrapped up in wires on the floor.
Bishop realizes that he has been tricked and ends the simulation. He goes over to Cable, who is on the floor, and tells him that he messed up, but the Fitzroy simulation was so real. Cable reminds him that it was supposed to feel real. Bishop helps Cable up, who tells Bishop that he knows all about obsessions. However, in their line of work, they cannot afford them.
In the control room Phoenix tells the Professor that Bishop was doing well until the end. The Professor tells Jean that it is the end that makes the difference. However, it is to Bishop’s credit that he realized his mistake and is taking steps to correct it. Jean asks the Professor if he is going to tell Bishop that. The Professor tells her that such praise must be first earned. The two telepathically appear before Bishop and Cable and the Professor tells Bishop that this is not the first time his obsession with Fitzroy has cost him. Bishop tells the Professor that Fitzroy was not a part of the program and that he cheated. Sarcastically, the Professor tells Bishop that cheating is something their opponents would never do. All he did was throw in a possible distraction. Bishop did the rest.
Moments later, Jean telepathically follows Cable out of the Danger Room to talk with him. Cable tells her that he understands how Bishop feels, when someone has hurt him the way Fitzroy has. Jean chimes in and addresses the point of how Apocalypse has hurt the two of them. Cable agrees and tells her that it is a hard thing to set aside. The other X-Men have no clue, for they live in the present. Bishop and he come from the future and have seen the world and how it is going to become. Now, they are trapped in a world where every move they make could either save the future or annihilate it. The two reach the men’s locker room and meet Gambit and Beast. Gambit apologizes to Jean and tells her that even in her astral form she still cannot go past that door. Beast walks in and asks for some privacy.
Later, after the six have changed into normal clothes, they drink some coffee, while Bishop explains how things used to be so simple. Fitzroy was a criminal and he was a cop. However, Fitzroy is a lowlife who always gets away. Gambit relates Fitzroy to Jean Valjean of Les Mis. Bishop tells Gambit that Valjean stole a loaf of bread, while Fitzroy is a killer.
The Professor reminds Bishop that Fitzroy is gone now and Bishop will find that there are many others who fit the same bill. He understands Bishop feels a sense of responsibility to the world he left behind, but his current home is in danger too. The threats are graver than ever. To fight them, the Professor needs a detective. In short, he needs Bishop. Bishop asks him if he will not take “no” for an answer. The Professor tells him that he never does. Bishop tells the Professor that he is nothing like the stories that survived to his time. Cable jokingly asks if he is better or worse. Bishop tells Cable that the jury is out, but he cannot help but respect the man. The Professor tells the X-Men that he has summoned them to a briefing, but are short two members. He then telepathically contacts Wolverine and asks him if there is a problem.
In the woods, Wolverine tells the Professor that there will be a problem if he does not get out of his head. He is busy hunting Rogue down. The Professor asks Wolverine if he requires any assistance. Wolverine tells him that he would rather do it alone, but the Professor reminds him that he and Rogue are needed badly. Wolverine asks the Professor to tell him something he does not already know. He asks the Professor to also let him do this on his own and give him some time.
Bishop asks the Professor if they should help. The Professor tells Bishop that there is a special bond between Rogue and Wolverine. In her current state, she needs someone who she absolutely trusts the most. However, there is only one other who can fit that bill and that is the reason that Xavier called them together; to discuss Mystique!
Xavier creates a telepathic image of Mystique and explains that there is a growing amount of evidence suggesting that Mystique is planning another assassination attempt on presidential candidate Robert Kelly. The X-Men must stop her at all costs and that is why Cable has been placed into Kelly’s inner circle to protect the man. Cable explains that it has been simple so far, but Bishop says that there is nothing simple about Mystique. Xavier agrees and points out that it is unlike Mystique to be so obvious. That means she may have a much larger goal than just to assassinate Kelly. They need answers and quickly. Given the consequences, they dare not fail.
Outside in what was only a few moments ago a lush and green forest, Wolverine finds himself standing in a katabatic ice storm that one would usually find in the Antarctic highlands. The wind and chill are enough to freeze a body solid in seconds. Fortunately, Wolverine has a healing factor, which makes freezing to death no problem. As Wolverine nears a cliff, a lightning bolt strikes the tree behind him. He slashes the tree away with his claws and mutters to himself that he does not feel welcome.
Wolverine continues his hunt and almost immediately comes to the end of the storm. He leaves the snowy field and enters a lush springtime forest, where no sign of the blizzard exists. Wolverine wonders if Rogue knows what she is doing. He finds Rogue in a clearing in the forest, sitting on her knees and holding her hands to her stomach. Wolverine calls out to her and Rogue asks him why he came. Wolverine sees that body fluids are seeping from Rogue’s hands and that a red bird is sitting peacefully on her leg. Wolverine tells her that he could not stay away and asks if she is okay.
Rogue cries and shows Wolverine her hands, as a set of bone claws emerge from both her hands. She tells him that she hurts and Wolverine comes over to her to tell her that he knows. Rogue asks him how he can know if she does not understand it herself. She is supposed to be invulnerable. She begins to hit herself in the head. She can fight the Hulk, but the claws won’t stop hurting. She asks Wolverine why it won’t stop. Wolverine calms her down and helps her pull the claws back into her. The two then hug once she does so.
Rogue tells Wolverine that she can feel her body trying to heal, but the claws won’t let it. As long as the claws are extended, the wounds stay raw. Wolverine tells her that he knows. Rogue realizes it has to be the same for him too and asks how he can possible stand it. Wolverine tells her that, when one does not have much of a choice, he must find a way to cope without giving up. Rogue tells him that the pain never ends and it is the worse pain she has ever felt. Wolverine reminds her that it is only pain and can be beaten with control. Rogue cries again and tells Wolverine that she has lost all her control. Everywhere in her head, there is only chaos and all he wants to do is drown in her screaming. Wolverine tells Rogue that giving up is not like her. She asks him what else she can do and Wolverine tells her to let he and Xavier help her.
On Muir Isle, a helicopter lands on the landing pad and Moira MacTaggart steps out and welcomes her foster child, Rahne Sinclair, who has been waiting for her. Moira tells Rahne that it has felt like ages since she last saw her and asks for a hug. Rahne welcomes her mother back home, but suddenly realizes that something is not right. Rahne smells other scents besides Moira’s and those scents are hostile.
In a flash, Rahne shifts into her werewolf form and attacks Moira, who reverts back into Mystique. Mystique tells someone to restrain Wolfsbane before she loses her temper. Sabretooth picks the girl off Mystique and tells her to calm down before he forgets that she is below his legal age limit. Wolfsbane bites Sabretooth and runs away back to the facility. Sabretooth tells her that, since she drew first blood, he gets to draw some more next time. Mystique tells Sabretooth to let the girl go. Sabretooth reminds Mystique that Wolfsbane will contact the X-Men. Mystique tells him that she hopes so; the more of them the better.
At Xavier’s mansion, the Professor explains to Bishop that Rogue has the ability to absorb the psyche and abilities of those with whom she makes skin-to-skin contact. Recently, she came in contact with a telepathic alien, which left Rogue’s powers devastated. The alien was a metamorph and that variation of her powers grafted itself to Rogue’s genetic structure. Now, she is manifesting the powers of anyone she has touched in the past. She now has some of Wolverine’s healing factor, as well as his claws. Unfortunately, she has no control whatsoever over these powers and, right now, they are unable to reverse the alteration. Rogue is truly the most dangerous mutant on the planet.
In the forest, Rogue and Wolverine meditate together to help Rogue control her new powers. Suddenly, a psionic image of the Phoenix appears around Rogue as Phoenix’s telepathy surfaces. Angrily, Rogue lunges at Wolverine with her claws extended, trying to get the voices in her head to shut up. As if out of control, telepathy is not enough, Rogue’s eyes begin to burn as Cyclops’ optic blast manifests itself. She warns Wolverine, but is too late. Wolverine is hit by the blast and pushed into a tree, which knocks him out.
Rogue gets up and tells Wolverine that she has tried to control the powers. Bishop rushes over to Rogue, as he sees her skin color turn indigo like Nightcrawler’s. Her arms turn into metal, like Colossus, and she begins to call lightning, like Storm. Rogue also is able to feel the Earth’s magnetism, like Magneto. This is only the beginning. Bishop grabs onto her from behind and tells her that it is over. He begins to absorb all the energy Rogue is expelling and channeling it through his body. As soon as Bishop touches her, though, he is already pushed to his limit. Rogue falls unconscious, as Phoenix and Xavier appear telepathically by Bishop, who helps up Wolverine. Xavier tells Bishop that he was brave, but could have been killed. He then tells Bishop that he and Jean will now use their telepathy to calm Rogue down.
Sometime later in the infirmary, Rogue wakes up and finds herself surrounded by Phoenix, Cable, Bishop, Wolverine and the Professor. She rubs her head and Jean tells her to take it easy, for she needs time to adjust. Rogue tells the X-Men that she feels normal and Bishop backs her up by saying that the bioscan reads normal. Rogue wonders how long that will last and Xavier tells her that it could be permanent. Rogue disagrees and tells the Professor that she can still feel the bone claws in her forearms, so at least that is permanent. Wolverine tells her that he is sorry, but Rogue tells him not to be.
The Professor tells Rogue that she was making good progress with Wolverine as her mentor. Wolverine asks Rogue what went wrong. Rogue tells him that she heard someone laugh in her head and, when she tried to respond, her head went nuts. However, she knows the laugh was from Mystique and she knows that the woman is on Muir Isle. Jean asks the Professor how Rogue could know that, but the Professor first tries to create a mindlink with Moira. Strangely, he is unable to.
Jean offers to add her telepathy to his, but Xavier tells her that there is some kind of interference that he has never met before and their effort will probably be futile. He then asks Rogue if she is sure. Rogue tells the Professor that Mystique is one of the voices loose in her head and she could recognize her anytime. Whatever Mystique is planning is bad and she is going to stop her.
Xavier tells Rogue that she is in no condition to travel. Rogue argues that Bishop said she was fine, but Xavier reminds her that Bishop is not in charge. Rogue tells Xavier that she is going, regardless of how she is feeling. Bishop tells Rogue that she is not going by herself. Wolverine agrees and tells Xavier that, if there is trouble, the three of them can handle it until the others arrive. If nothing is wrong, then they will come right back home. Jean turns to the Professor and tells him that it is his choice. Xavier thinks about it and tells the others that they have his blessings. He wishes he could offer more help, but right now the X-Men are needed to maintain coverage on Senator Kelly.
In Boston, Senator Kelly stands in front of the Faneuil Hall on the eve of the election. From the amount of media vans parked, it can be arguably said that the whole world is watching. Kelly begins his speech by explaining how their ancestors made a stand against tyranny in the past. Once again, their birthright is threatened. Mutants are too dangerous. In fact, one was so feared of that the United Nations gave him his own country. Due to this, the world must now fear itself. However, that fear cannot be denied or ignored. The question now is, what they are going to plan on doing about it?
Cable, using telepathy to disguise himself, listens to Senator Kelly’s speech and criticizes Kelly for blaming mutants when it means he will be condemning the children of the world. Cable questions whether it is right to protect a man like Kelly. Nearby, Gambit and Beast ask Cable if everything is good so far. Telepathically, Cable says everything is fine if you ignore the speech. The Secret Service has done their job well and the interior of the hall is secure. Beast asks Cable if he can scan the plaza for threats, but Cable tells him that he is already using most of his power to disguise himself, so he cannot spare any to scan the crowd.
Over the Atlantic, Rogue flies through the air, carrying a rope, which holds Bishop and Wolverine. Rogue tells the two that the trip will be quick, but it will be miserable for them. Wolverine says that he should have brought a coat, while Bishop says that he should have had his head examined. The two hold their breath as Rogue goes sub-orbital. Some time later, as Senator Kelly nears the end of his speech; Rogue starts the re-entry and sees Muir Isle. She warns her passengers to treat the mission as a combat insertion into a hot zone. They cannot take any chances.
In Boston, Kelly tells his supporters that he knows the risk of what will happen if they confront mutant kind. He was almost killed once and his wife was killed by the repercussions. However, in the past months, he has gained a sense of what mutant kind means to the people of America. Suddenly, Kelly tells the people that it is easy to give into fear and to lash out at those they hate, to destroy what they don’t understand. “But, my fellow Americans, my fellow citizens of the world,” says Kelly, “it would be WRONG!”
Before Kelly can elaborate any further on his sudden change of heart, there is an explosion, as the front door to the whole is blown away. In the dust, a group of figures appears, with one ridiculously large man in the front. The Blob enters the room and introduces the Brotherhood of Mutants to the people and tells the senator that they have some unfinished business.
“We’re too late!” screams Rogue, as she approaches Muir Island, which explodes and is removed off the face of the planet!