A massive and dangerous storm rages over the Atlantic Ocean. Off the coast of Cape Wrath, the northern most part of Scotland, a jet streaks across the sky in a desperate attempt to get back to the Xavier Institute for Higher Learning in New York. Turbulence hits the jet, which would at one time have been housed at Muir Isle, a research center headed by Moira MacTaggart. Thanks to Mystique, though, that island does not even exist anymore. The X-Men aboard the jet came away from the island with a victory, technically. However, their victory came with casualties and, now, they are on a mad race against time to save those injured.
Bishop, in his tattered uniform, sits at the controls of the plane, trying to guide it through the dark skies that precede the storm. Behind him, Wolverine, with his shirt gone, stands above the mortally wounded Moira MacTaggart, who lies on a bed in her clothing, or what’s left of it. Rahne Sinclair, a.k.a. Wolfsbane, holds her foster mother’s hand and cries, praying that the woman does not die. Rogue stands to the side and watches Wolverine, as he sets up the IV bag for Moira.
Bishop tells Wolverine that it is a miracle that the jet even took off, considering its condition. Wolverine tells him that miracles are their stock in-trade, but Bishop tells him that he is being serious. Hazard readings for the engine and controls are going off and he is not sure if they have enough fuel. Rogue tells Bishop to deal with what he has and reminds him that Mystique has mutated the Legacy Virus so that it will only affect humans. Moira has the cure, but it is locked in her head. The X-Men need to save her to save the world. The X-Men call themselves heroes. Now, they need to prove it.
Rogue pulls out a first aid kit and volunteers to stabilize Moira’s vitals and to repair what they can of the worst of the damage. Rogue goes to Moira’s side and tells the others that the woman has no broken bones, but she has many puncture wounds, lacerations and internal injuries. She tosses another IV to Wolverine and tells him to hook them up to Moira’s veins and to find a whole unit of blood for her. Rogue then gives a bio-monitor to Rahne, so she can give Rogue a running report on Moira’s vitals.
Suddenly, the jet hits an air pocket and all those standing fall. Rogue covers Moira with her body to prevent anything from falling on the gurney. She tells Moira that they will get her through this. When the turbulence ends, Rogue tells Bishop that he needs to get the jet to the mansion as quickly and steadily as possible.
Rogue notices that Rahne is staring at her and asks her what is wrong. Rahne tells Rogue that she is bleeding from where Mystique stabbed her. Rogue solemnly tells Rahne that she should be dead, but it looks worse than what it actually is. Mystique did not know that her powers were out of control lately. She has been displaying the powers of people she has absorbed in the past. Wolverine’s healing factor is one of the more permanent ones. She is now as hard to kill as he is. Still crying, Rahne asks Rogue if she could pass some of that blood onto Moira so she can heal.
Rogue apologizes and tells Rahne that it was once tried before with Wolverine’s blood. The healing factor does not work that way. They need to save Moira the old fashion way and pray that everything turns out okay. However, she needs Rahne to be brave. Rogue tells Rahne that, since she is their resident church girl, she should start praying, though the young Scots girl tells Rogue that she has been praying since take-off. Wolverine asks Rogue if she can handle it. Rogue asks him if he sees anyone else around who can do better.
Weakly, Moira tells Rogue that she presumes that the girl knows what she is doing. Rogue tells her that she has no clue and is making it up as she goes. In what may be a joke, Moira tells Rogue that she feels reassured. Rogue tells Moira that Cecelia Reyes is a trauma surgeon. A short time ago, she absorbed Cecelia. The memories and skill are still fresh in her mind. Though Rogue’s mind is blank, her hands know exactly what to do. Moira tells Rogue that she believes and trusts in her. Before Rogue begins, she tells Moira that they have no anesthesia, but Wolverine knows some neural pressure points. It won’t be pleasant, but it will be bearable. Moira tells Rogue that, considering the alternative, she is in no position to complain.
Rogue turns to Bishop and tells him that she is going to start major surgery to save Moira’s life. She needs no bumps. Bishop tells her to ask for the sun, the moon and the stars while she is at it. Better yet, he tells her to look out the window to what is ahead. Wolverine looks out the window, as the jet nears the massive storm, which is raging over the Atlantic Ocean. Wolverine asks Bishop if they can climb over it, but Bishop does not believe that they can. Wolverine tells him to go around, but Bishop points out that it will add hours to their flight time. Either way, they are likely to lose. The radios are also smashed, so they cannot call for help. Wolverine reminds Bishop that Xavier and Jean are telepaths. All they need to do is to yell with their thoughts. The X-Men need to deliver Moira and her cure. Failure is not an option.
Rogue begins the surgery and pours all her concentration into it. Wolverine notes that Rogue is cutting like a pro. He then realizes that she forgot all about him. He looks back into the next room of the plane, where the unconscious Mystique is strapped to a gurney. Wolverine goes over to Mystique and tells her that they have known each other for a long time. They were almost friends once, but that is over. The woman he once respected is dead. She cut down her own daughter, without giving it a second thought. She was willing to kill millions to create her own version of mutantkind’s salvation. Rogue can forgive her, but he won’t.
Wolverine extends a single claw and pulls his arm back to kill Mystique, when, suddenly, Rahne comes into the room. Wolverine quickly pulls back his claw, as Rahne tells him that he is needed. Wolverine tells him that he only needs a minute, but Rahne tells him that Rogue needs him immediately. Wolverine leaves the room. Rahne looks at Mystique and tells the woman that she could not allow this. She tried to kill her own daughter and may have killed Moira. Before Mystique neutralized Rahne’s powers, she could turn into a werewolf. Mystique is the true monster, though. Rahne swears to Mystique that her life will be taken by her but, first, she wants to make sure she hears the shape shifter scream.
Back at the Xavier Institute, a jet lands in the hangar. Archangel, Psylocke, Phoenix, Gambit, Storm and Iceman wait for the occupants to come out. Beast jovially leaps out of the Blackbird and tells the X-Men that they won. He is proud to announce that Blob and his Brotherhood of Mutants bombed. Iceman tells his friend that it sounded like a fun fight. Beast tells him that it, honestly, was not. They did defeat the Brotherhood, but it was Pyro who saved Kelly and died in the process. Bobby realizes that it is horrible, but hopes that maybe Pyro’s sacrifice will change people’s minds, as it seems to have changed Senator Kelly’s mind. It would be great if Kelly would believe that humans and mutants could live in peace. The future may not be so bad after all.
Colossus exits the Blackbird and asks Iceman if he truly feels that one person can make a difference, no matter how well intentioned he is. Beast tells Colossus to look around, for Xavier is one man and look what he has accomplished. Colossus asks Beast how many of their comrades have died in the process and how many will die in the future. He then asks him how much as really changed. Trust is something that takes effort to make. It is much easier to hate instead. The X-Men celebrate because they were victorious but, in the end, the police were just as ready to arrest them as they were ready to arrest the Brotherhood. The good is always overlooked, while evil defines them all. Beast has a great dream, but Colossus chooses to live in reality. A legacy to pass to his children is what gives meaning to the death of his brother and sister. “The rest is dust.”
Colossus leaves the room, leaving Beast perplexed. Nightcrawler approaches Jean and asks her if there has been any word from Muir Isle yet. Jean says not yet and asks where Cable is. Nightcrawler tells her that he has some unfinished business with Senator Kelly.
In Boston, Cable, in civilian clothes, thanks to his telepathy, finds himself standing in front of the grave of Sharon Kelly, the late wife of Robert Kelly. Senator Kelly and his guards arrive and Kelly is surprised to see Nathan. He asks him what he is doing at his wife’s grave. Cable turns to face Kelly and tells him that Sharon is what this is all about. Decent people like her are caught in the middle of a struggle that has nothing to do with them. Cable tells Kelly that he was married once. His wife was his hope and fulfillment. He saw her killed.
Kelly tells Cable that he is sorry. Cable tells him that time heals all wounds, or at least that is how the saying goes. Kelly tells Cable that he has been apart of his life ever since the campaign had begun. Cable tells him that he has been watching his back. Kelly asks him why, as he shares a cup of coffee with him. Cable tells him that, in history, he is a crucial figure.
Kelly tells Cable that he speaks as if he is from the future. The telepath tells the man that he is not joking. Kelly tells him that, after what he has seen in the last twenty-four hours, he believes him and then asks Cable if he knows how all of this turns out. Cable explains that, in his time period, most of the history was lost. However, he does know that Kelly is an important man. It is a gamble to assume that saving him is for the best, though. Hearing this, Kelly asks Cable that, if things were otherwise, would he be here to kill him. Cable tells Kelly that he is a soldier and cannot take his mentor’s dream for granted.
Cable tells Kelly that the senator has no idea what forces are at work around him or the repercussions of his actions. When he was a baby, he was kidnapped by a madman, who inflicted him with a fatal disease. To save him, Cable’s parents threw him down the time stream in hope that the world of the future could save him. The man standing before Kelly is the end result. Cable explains that Magneto and Mystique do exist and that the X-Men are there to stop them. Change has already occurred, whether they like it or not, but it is not the end of history.
Kelly tells Cable that, even as heroes, they still wear masks. Cable asks the man that, given the history of the world, how is that a surprise? Kelly asks Cable if mutants are just as afraid as humans are. The telepath explains that mutants have just as much to lose as humans. Kelly then asks Cable if they can just all think of what they all have to gain. He then asks Cable to end the charade and to let him see the real Cable. Cable ends the illusion and allows Kelly to see the real him, much to the surprise of the guards. The two men shake hands and Kelly tells Cable that they have just created a foundation on which they can build upon.
Over the Atlantic, Rogue goes over to Bishop, who asks her if he can do anything for her. Rogue asks him if he can make the plane go faster, though she already knows that he can’t and that it won’t make a difference. Bishop asks her if it is that bad. Rogue tells him that she did what she could, but she has no more ideas or skill. That is the curse of medicine; nature cannot be beaten. “Damn,” says Bishop. “Yeah,” responds Rogue.
Rahne goes to Rogue and tells her that Moira is asking for her. Rogue returns to Moira, who weakly tells Rogue that there is not much time. Whatever happens to her, the cure for the Legacy Virus must not be lost. Rogue agrees and begins to take off her glove, but Moira tells her to stop. She saw the initial data on her condition and knows that her mind is too chaotic to risk a download. Moira’s body is also messed up and she would most likely not survive long enough for the transfer to end. The data is complex and there is no room for error. Rogue asks Moira what the alternative is. Moira begins to cry her last tears and tells Rogue that they must contact Charles at once.
At the mansion, Colossus feeds hay to the horses in the stable. Xavier approaches Colossus, who tells his mentor that he apologizes for speaking out of line in the hangar. Charles tells Colossus that he is a poor teacher if the only thing that his student learned was to keep silent. Colossus asks the Professor if he ever thought, when he was young, that his life would turn out this way. Xavier tells him that he cannot remember when he was even young. It is he who should apologize anyway, for what he has done to Colossus.
Colossus smiles and asks him if he is apologizing for taking a Siberian farmer and showing him the stars. Xavier tells him that he had dreams. Colossus corrects him and tells him that he still has dreams. Sadly, the Professor tells Colossus that he had no right to replace the young man’s dreams with his own. Colossus tells Xavier that he chose to join the X-Men, just like how he chooses to stay. As a farmer, he dreamed of good weather but was often disappointed. He also dreamt of spring, but knew that a desolate winter must first pass. The Professor has a good dream that they must build upon. Colossus has the strength to build and the Professor showed him the best way to use that strength. It is the same for all of them. Xavier tells Colossus that, if that is the case, then they should return to the mansion, for there is much to be done.
In Boston, a news conference goes on, explaining that, even after the events of last night’s assassination attempt, Senator Kelly will be making a speech within the hour. The media starts to ask question to the woman making the announcement, Angela, and asks questions, such as if Kelly is quitting the race, if he has spoken with the President, if he is planning on reversing his stand on mutants or if he is being influenced by mutants. A Kelly supporter in the back tells a woman that he found a copy of Kelly’s speech that was interrupted by the Brotherhood and it seems that he was going to talk nice about mutants. The woman cannot believe the man, for it would go against everything Kelly stands for.
In his room, Kelly tells his people to give his complements to Angela for the way she handled the crowd. Another woman, Sharon, asks the senator to reconsider giving a speech but Kelly tells her that it is out of the question. He can and has to do this. Cable, disguised in a suit, tells Kelly that the danger is real. Kelly tells Cable that his mere presence already told him that. He then asks Cable if he is going to be his bodyguard his whole life. “If that’s what it takes,” says Cable. Kelly then tells him that he owes it to Cable and the future to be worthy of that obligation. Suddenly, Cable “hears” something in the distance. Kelly asks him if something is wrong. Cable tells him that he is not sure, but it sounded like someone was crying out in the distance. Whatever it was, it’s gone now.
Over the Atlantic, Moira calls for Charles in her mind. Desperately, she wonders why, this once in her life, he cannot hear her. As tears pour out of her face, she begs Charles to answer her. Bishop tells everyone that they have reached the home stretch and that they should be home within the hour. Rogue pulls off her glove and tells Bishop that Moira won’t make it. Wolverine tries to stop her but Rogue tells him that they do not have a choice. Her vitals are barely registering. She is alive by her own will. At least, now, they have a shot at saving the data, rather than losing it all. Rogue goes to touch Moira on the face and tells her that the fight is over and that it is time to rest. Moira tells her that it is over when she says and desperately calls out to Xavier for the last time.
At the mansion, Xavier hears Moira and screams out her name and asks her what has happened to her. He orders Colossus to take him to Cerebro at once. At Cerebro, Xavier tells Jean and Storm that Moira is terribly weak and is reaching out to him with that last of her strength. The only way to reach her and do what is necessary is to use Cerebro to augment his powers. Beast arrives and asks Storm why the Professor sounded the alarm. Storm picks up Beast and uses her winds to fly them out of the mansion at top speed. She explains that Moira has found a cure for the Legacy Virus, but is critically wounded. She hopes to transfer the information to Xavier from her mind to his. The Professor has a telepathic fix on her, but Storm can get them there the fastest, so Beast can use his medical skills to make a difference.
As Xavier leaves his body, he is amazed that even though Storm and Beast know that they will not make it in time; they still try their hardest. After all the years of struggle and setbacks, the dream is still worth fighting. For everyone’s sake, they must prevail. Fortunately, distance means nothing to the speed of thought and, in moments, Xavier is at the jet over the Atlantic. He enters the jet and sees Moira’s essence hanging over her dying body, waiting for him. Moira thanks the heavens that Xavier has reached her but, when the two near each other, their connection is shattered.
At the mansion, Xavier falls out of his wheelchair. Jean and Nightcrawler rush to him to help him up. Nightcrawler tells Xavier that, in the last moments, he flat lined. Xavier explains that he underestimated Moira’s condition and that she is weaker than he expected her to be. They could not establish a mind link. Jean tells him that the two of them will go back together with Cerebro. The Professor tells Jean that he refuses to let Jean witness the death of another person on the astral plane again. Jean puts on the Cerebro headpiece and tells Xavier that she was a girl back them. Now, she is grown up. Xavier thanks Jean, as the two try to make a connection with Moira again.
Xavier and Jean reach Moira, whose essence is still waiting over her dying body. This time, they do not fail. Xavier and Moira embrace each other, as the background behind them disappears, leaving the three of them in a void. Xavier asks the love of his life how this happened. Moira tells him that what happened has happened. They cannot dwell on what cannot be changed. Instead, he needs to focus on what really matters now.
Xavier and Moira passionately hold on to each other in their final embrace. Jean looks at the two, who were once young lovers. Their troubles melt away in each other’s arms, until only the essence of their two souls remain. They truly become one as Moira passes on the data to Xavier. Xavier and Moira kiss one last time and the two begin to glow. Terrified, Jean realizes that she has seen that kind of radiance before.
On the jet, Wolverine tells Rogue and the others that Moira is flat lining. At the mansion, Nightcrawler checks Xavier’s vitals and realizes that something is wrong, for the Professor’s life signs are dropping “We’re losing him!” yells Kurt.
Half a lifetime ago, Jean held her best friend in her arms while she died. This was the first time she saw this light. Jean tries to pull Xavier and Moira apart but realizes that the Professor loves Moira too much and won’t let her go.
At that same moment in Boston, Senator Kelly begins his speech. He tells the nation that he began his campaign, talking about fear, but it is fear that is the enemy. Cable watches the crowd and is happy to see that they are actually listening to him. Suddenly, he hears Jean calling his name and realizes that Xavier is in trouble. Kelly pauses and, in his head, asks Cable if everything is all right. Cable tells him that he is needed elsewhere and that he will be quick. Kelly tells him not to worry and that he will be fine. Kelly turns back to the audience, full of college volunteers, and tells them that they need to take a stand. The world has too often passed violence down from generation to generation. It must stop now.
Cable telepathically reaches Jean, who apologizes for taking him away from Kelly. Cable tells her that, if they do this right and quick, no one will know that he was gone. The two again try to separate Moira and Xavier, but find that he won’t budge. Cable tells Jean that dying is easy when you can face eternity in the arms of your first true love. Cable asks the Professor if he thinks that this is what Moira wants. It is her time to go. It is her sacrifice. If the Professor yields to temptation, then he will make it nothing.
Jean tells Xavier that she knows how he feels. She felt the same way when she could only helplessly watch as Scott sacrificed all to defeat Apocalypse. She would have given anything to save him then, almost as much to join him. However, she has too much to live for and so does he. It is his dream that they are fighting for and, without him, it is dust. Without him, the X-Men are no more.
Moira pulls away from Xavier and hovers above the three mutants, beautifully, before them. She tells Xavier that he should listen well to those who love him. She asks him to make all of them proud, including her. Xavier reaches out to Moira and calls her back. A bright light appears behind Moira. She tells Charles that, with him, she has known joy. Even with the mistakes they have made, she has no regrets. The light intensifies behind Moira so that only her silhouette can be seen. Moira tells Xavier that she is not afraid. He cannot imagine the peace and beauty she feels here. “I love you, Charles Xavier,” says Moira, as she speaks for the last time, “an’ I wish y’ well – until we meet again.” Moira is enveloped in the light, which disappears, leaving the three X-Men alone.
“She’s gone,” says Wolverine as he covers Moira’s face with a blanket. Jean turns to Cable and Charles and asks her distraught companions what is wrong. Charles senses a threatening thought. Cable realizes it is coming from near Kelly and returns immediately to his body.
“GUN!” screams Cable, as he casts down his illusion and jumps in front of Kelly. It is too late, though. A young man in the crowd calls Kelly a race traitor and fires four rounds into Kelly’s chest, as he is tackled by a group of Secret Service agents. Cable reaches Kelly at the last second but is too late.
Cable holds the dying Kelly in his arms. Kelly tells him not to hurt the boy, because he is just a kid. It is his own fault, for not understanding sooner. Cable tells Kelly to stop talking and to conserve his energy. He then calls out for someone to call the medics and an ambulance. The dying Kelly tells Nathan not to give up on his dream or on humanity. “We’re a young species, we make mistakes. But give us a chance to grow…” says Kelly almost inaudibly, “…we may…surprise you…yet…”