The movie starts with a caption reading Ottawa, 1961 where Wolverine (who looks much less hairy and happier) is walking through an alleyway, while a man in a hat and long coat follows him. As they both walk, the man yells out "You have quite an extraordinary gift." Wolverine turns around and when he says that and simply replies "I beg your pardon?" Wolverine then asks who he is and the man replies saying it isn't relevant. He gets closer and says how Rapid Cellular Regeneration is a very rare and powerful Mutation and that will be very useful in the "tests". Wolverine tells the man to stay away from him, but before he can leave two soldiers grab him while the man injects a needle into Wolverine's neck. The man takes off his hat revealing himself to have a strange, red, solid diamond engraved into his forehead. He tells the soldiers to take Wolverine into the van and back to the laboratory, they listen without a word and load him into a special Jet with the words Essex Corps on the doors. It cloaks it's self with the background and flies off into the sky.
Roll Credits and Title (with this playing)
It shows Wolverine being experimented on, injected with metal, slashed and healed, while Mr. Sinister simply watches it happen. A caption reveals it to be present day and Wolverine wakes up in the middle of the night with his claws emerged, breathing heavily. He retracts them and gets up, going to the school gym. He practices while there until a new student, Jubilation Lee comes too and asks if he "can't sleep either"? He asks if she's a new student, and she introduces herself and Wolverine asks what he power is.
She creates Firework like blasts in her hands and shoots a weight set. Wolverine then comments on the absurdity that she can generate fireworks, but she points out having metal claws and mutton chops aren't normal either. He says touche and the two talk some more. The next day in Washington D.C. Jean Grey is discussing how she wants the Purifiers to be officially labeled as a terrorist group, but Warren Worthington Sr. argues against it, saying how he for one thinks they are just people trying to fight against tyrants like Magneto, and other enhanced people across the globe. He brings up the destruction caused in New York from Gravition, or Athens by the Maximoff Twins. But Jean Grey says how there have been recent kidnappings of Mutants across the country, and she believes the Purifiers must be responsible, that even if they're Mutants they're still United States citizens who need support and protection.
In Northern Canada, at a mysterious base a man is doing Scientific research with maps of locations all around the world. It is revealed the man is Mr. Sinister, who has not aged at all in the past 50 years. He continues to put in calculations and look at the maps until he sees a location appear in Louisiana. Where he says under his voice "I finally found you. The Holy Grail of Mutations." He goes into one of the laboratories and opens up different cages letting his latest subjects come out. Including Marrow, a Mutant with the ability to shoot and shape bones that come out of her back, Deadpool a warrior armed to the teeth with guns and swords who has severe psychological trauma, and Sabretooth, a feral Mutant with razor sharp claws and enhanced strength.
He tells them that he has a mission for them to do, find and capture a Mutant located in Louisiana, that this would be one of the most significant portions of the plan he has involved them all in. He warns them not to disappoint, that Essex Corps broke and re-built them for a reason.
It shows at the X-Mansion the team in the middle of an intense combat routine. Wolverine, Jubilee, Storm, Iceman, Angel, Colossus, and Nightcrawler fight as hard as they can eventually destroying a large Sentinel, only to reveal it to be a Danger Room sequence. And Cyclops walks into the room and explains to them what they could do better and how they need to improve. Wolverine says how they were fine and needs to stop being so uptight, but Cyclops doesn't take the bait and just tells them to keep practicing their teamwork.
He heads outside through the school hallways to see Jean and Beast returned from Washington D.C. saying how the Government has refused to help them deal with the Purifiers terrorism. They all go to find Professor Xavier, and he tells them if they are refusing to protect Mutants the X-Men have a greater responsibility to do so themselves. Professor Xavier says using Cerebro, he has detected that the Purifiers are beginning to head into the deep south, and would likely hit New Orleans Next. He needed an X-Men team to go down there and stop them from hurting any innocent Mutant in the city, as quickly as they can.
In New Orleans, it shows a young girl walking through the slums with a white streak through her hair, she is revealed to be named Anne, and works as a waitress serving inside a casino while her boyfriend, Remy, plays poker at one of the tables. They try to leave for the night before they start to get harassed by a group of Purifiers while Remy fights them off with his staff, and his Mutant powers to super-charge objects with kinetic energy, Anne just runs off. She ends up running into the X-Men who ask where the Purifiers are so they can stop them.
An all-out Brawl starts with the X-Men and Remy fighting against the Purifiers until a third group comes in and takes out the last of the Purifiers, Wolverine recognizes them as the Essex Corps Mutant Fighters. He exchanges a few harsh words with Sabretooth before fighting him, and Nightcrawler tries to fight Deadpool both teleporting everywhere. While the battling happens, Remy starts charging Poker cards and shooting them at both X-Men and Essex Mutants. While Anne accidentally touches Storm, which weakens Storm exponentially and causes Anne to "absorb" her power temporarily, she uses the wind manipulation to fly her and Remy out of there not wanting to be caught up in any of this. The two teams fight each other they notice her gone, and start trying to look breaking up the conflict.
At the X-Mansion the team is explaining to Professor Xavier and Moira MacTaggert what had happened and with Remy's abilities how Anne "copied" Storm's ability which temporarily damaged her, but she seemed fine now. Wolverine (who been silent the entire time) says how he knows who the people after them were. The Essex Corps, the same people who covered Wolverine's bones with Adamantium and erased his memories years ago. The man leading the operation, who everyone called Mr. Sinister was rounding up Mutants and experimenting on them to "improve" them in the most twisted ways they can imagine, just to use them as weapons. Wolverine then says how he barely made it out alive, but remembers the strong rivalry he had with fellow Experiment victim, called Sabretooth, who he fought in New Orleans. The Professor says that they need to find the two young Mutants who the Essex Corps must have been after, Cyclops and Jean agree.
Angel and Iceman wonder why the X-Men don't just "call the Avengers" to try and fight Sinister and his Corps, but Beast points out how the Essex Corps must be an underground organization and without sufficient evidence of their existence, The Avengers would never go after them, that this is something they need to handle on their own.
After everyone leaves Wolverine wishes to speak to the Professor alone. He says that he is deeply disturbed by the team trying to combat the Essex Corps. Professor Xavier says how he can get bits and pieces of Wolverine's pain and fear he experienced there, and thinks it would be best if he sat out of there mission, not wanting him to get too emotionally involved. Wolverine leaves and he tells Jubilee what the Professor wants him to do. She says how ridiculous it is since he's been a member of the X-Men for awhile now and should be able to fight these guys, and how Xavier can't do that. But Wolverine says he's a whole lot wiser then he is, and maybe it's better just to leave this be. He's never been as strong as Sabretooth, and doesn't even want to see Mr. Sinister again, he never wanted to see that demented "freak" ever again.
The clip then shows at the Essex Corps facility Mr. Sinister continues to do his lab work, while examining his warrior's in their cells (wondering if Deadpool ever actually shuts up) and takes notes accordingly. But in the middle of that, it shows Professor Xavier in New York using Cerebro to try and locate Sinister himself, but back in Canada the Diamond begins to glow on his forehead as he starts resisting the Professor's power. Inside a mental state, Mr. Sinister chuckles and asks Professor Xavier if he seriously thinks he can violate his mind. If he's that weak, like the other pathetic enhanced people he's come across. Professor Xavier asks him what he did to Logan, and why he's causing so much pain to innocent Mutants around the world. He tells Xavier how "he wouldn't believe him if he told the truth" the two argue for a little bit longer, before Sinister grows tired of the conversation. He says he's done speaking, and actually forces it to stop, causing Charles to yank off the Cerebro head piece in pain, shocked by Sinister actually turning his Telepathy on him like that.
In the middle of the deep south, Anne and Remy are going through a small town. Anne says that they need to lay low from these people going after them for being different, and there's only one place she knows they can't look. When he asks where, she knocks on a door and her parents answer, they try to hug her and she moves away saying how she is in a lot of trouble and needs help, they reluctantly let her and Remy in. She explains how it will only be a couple of days tops, maybe weeks. But her parents explain they aren't comfortable with two "Muties" living under their roof, and say they're only letting her stay because of their family values, and they want her gone as soon as possible, it hurts her but she seems to understand, Remy is upset though.
The X-Men spend the next couple of weeks fighting against the Essex Corps and their Mutants in multiple places (with Wolverine sitting out and smoking cigars), saving different Mutants, both looking for wherever Marie and Remy could be hiding out in. Professor Xavier continuing to try and use Cerebro, but continues to get adversity from Sinister's powers. At the X-Mansion, he is trying again while Jean Grey walks in. She says how she has been practicing strengthening her Telepathy, and maybe together they can override Sinister's defenses and find Anne. He agrees to it, and even with Sinister's strength the two Telepaths manage to overpower him and locate Anne and Remy staying at a house in rural Mississippi. Professor Xavier prepares to leave and try to save the young Mutants with Jean Grey's help, Wolverine tries to stop them saying how they don't know how dangerous the Essex Corps are, but they do not listen and go anyway. After contemplating it, Wolverine (with Jubilee's help) sneaks on board the X-Jet as they fly to the south.
In Canada, Mr. Sinister realizes that Xavier has found the location of Anne Marie and Remy LaBeau, determined to confront them he takes his own means of transportation and a handful of soldiers to finally capture them. In Mississippi, Anne opens the door and sees Professor Xavier standing outside. He tries to talk to her and her boyfriend to join the X-Men and shows acceptance for their "gifts" but Mr. Sinister and Sabretooth show up too, and Sinister express how it's nice to finally see Xavier in the flesh, but that the two Mutants were his. He sends Sabretooth to try and get Anne but she touches him and absorbs his ability, of Rapid Cellular Regeneration and Sharp Claws, her and Remy to fight off Sinister but with his rapid reflexes and energy projection he beats them both (revealing to be unaffected by Anne's power because he isn't an organic Mutant).
While Mr. Sinister fights Jean for awhile, he is about to hurt her until Wolverine comes out of hiding and tries to attack Sinister, who quickly stops him, Marveling at how "Weapon X" was still around and had returned to him. He picks up Wolverine by his neck and says how he's done with him, and that he has a new Mutant that he convents, someone who is superior even to him. Wolverine swears he will destroy Sinister and the Essex Corps, but Sinister says that it's simply Survival of the Fittest, and the Strongest Will Survive. Not him. He throws Wolverine down to Sabretooth's level, where they both fight shortly. Anne is then taken and flown away in the jet from the entire town.
After reorganizing Jean is furious with Logan, saying how she could've held Sinister back and had the Professor taken Anne and Remy to a safe place, but because of his desperate longing for revenge she's gone now and they have no idea what Sinister will do with her. Cyclops agrees with her, and wonders why Logan cared so much he couldn't even see Jean get hurt in a fight, even one she might've won, but he just swears at them and says how Mr. Sinister ruined him, and is still doing it and will take down the X-Men too. Remy, who's there says how they need to get Anne back, plain and simple. If someone in New Orleans if a rival took a precious prize from him, he would go to his house and take it back.
Beast says how in Sinister's and the Essex Corps arrogance, they seem to have neglected the detail of shielding their location from Cerebro, and can easily be found through it now. Professor Xavier locates Anne Marie in Northern Canada, the exact location, built right next to Alkali Lake, in the Northwest Territories (Wolverine shutters hearing the name). The X-Men get ready for it, and despite Cyclops protesting it the Professor has changed his mind, and now wants Wolverine to go on this mission to help make this right, and the conquer the demons that still haunt him from Sinister's cruelty.
In the Essex Corps, Anne Marie is being experimented upon by multiple scientists as Sinister watches. He goes down and says how he is amazed by her powers and strength, commenting how she is truly the greatest piece of Darwinism he has seen in all the years he has been in Science. She asks him why he's doing this, and what he wants. Sinister sits down and says how he figured out the meaning of life, with the help of his "mentor". That Survival of the Fittest rules this world. It is how evolution is, and has always been, the strong rule over the weak, and that is what Mutants are, they are strong and everything else is weak. He says that Anne Marie is strong, but he's stronger and will use her Ability Replication genes to implement any powers he wants in a group of kidnapped people (including Angel's father, Warren Sr.). He further explained once his subjects are fully under control he will use them in the great conquest to purge off the weak and usher in the Apocalypse, a new age in evolution. He starts walking off as his scientists cut into her more, and he walks away laughing maniacally.
The X-Men are flying to Canada in the X-Jet while Cyclops is talking to Jean, and everyone generally seems to be largely nervous and uptight about the situation. As they keep flying, they start to notice missiles beginning to follow them. Believing they're from the Essex Corps, they try and get them off and use their powers to stop them, they just keep coming and eventually one hits the Jet and causes them to crash-land in the middle of the Canadian wilderness. As they get out, they see the Missiles were being controlled by Magneto and the Brotherhood who is waiting for them in the forest. He says he is not looking for violence, and simply wants to speak to them.
When they back down and ask what Magneto and the Brotherhood even want, he says that he knows about the Essex Corps and thinks what Mr. Sinister is doing with Mutants, experimenting on them, using them as weapons, trying to take over the entire planet for his own ego is deplorable. He also says how the the Purifiers have taken a much stronger toll of the Brotherhood recently, and he has not wanted Mutant-kind to divide amongst it's self any further. They need to stick together, if they are to survive, starting with fighting Sinister and the Essex Corps. They are skeptical but ultimately agree to Magneto's help bargain and continue on their journey. In the Essex Corps, Marrow is watching outside with the guards until she sees the X-Jet coming towards them and begins to create sharp, projectile bones, and begin to shoot them.
They send out Angel to deal with her and the two get into a semi-large brawl. Inside the building Sinister is injecting the subjects with Anne's genes. While he is informed that there is a break into the facility, he is angry but simply tries to stay collected and demands Deadpool and Sabretooth try and hold them back, until he's done with the experiments.
The X-Men and Brotherhood members raid the Facility, while Deadpool manages to get in a fight with Remy (now nicknamed Gambit by the X-Men) and Iceman. They manage to beat him and knock Deadpool into the middle of the freezing lake. Wolverine, Jubilee, and Beast try to fight Sabretooth, with Wolverine finally besting his nemesis and all of them continue trying to find wherever Anne is being held at. Wolverine opens a door and goes into the very place he had his claws placed on him, and starts to have invasive, PTSD-esque, flashbacks of it happening to him and his traumatic escaping. Mr. Sinister is standing there too and tells Wolverine, how he remembers. Even with the attempts to block out his memories, some little ones slip through the cracks. Wolverine swears he'll kill Mr. Sinister. He laughs and says that he used to think James (Wolverine's real name as he reveals) was one of a kind, and could never be replicated, but that he was very much wrong.
He presses a large button and out of a chamber comes a female Mutant with two claws coming out of each of her hands. Mr. Sinister tells Wolverine that she is Weapon X23, that there have been a lot of attempts made to clone him and she is the first one that he perfected. He says "enjoy" and leaves while the two start to fight. Angel is sneaking through the facility and ends up finding his father, who says he regrets being so hateful towards Mutants, and is proud of his son for being a hero. Before Angel can try to fly him out Mr. Sinister attacks Angel, and knocks him out along with his dad. Shortly afterwards he starts the sequence to give powers to all the other test subjects, much to Anne's pleas not to.
Wolverine bests X23 and meets up with the other X-Men. Cyclops (with his Optic Beam) blasts through the door into the main chamber and they all confront Sinister, who tells them that it's already too late and in a matter of time he will have brainwashed and transformed all of those people into his own super powered army, and comments on how Evolution wins again. But shortly after one of his "scientists" kicks Sinister out of the way and turns off the brainwashing process, though they still had powers, it ruined Sinister's plans. The "scientist" shape shifts revealing herself to be Mystique, who also releases Anne Marie from her binds.
Mr. Sinister screams in rage as the newly powered people start causing chaos, and says how the X-Men ruined everything and will now die with the beings they helped create and quickly manages to escape outside. The X-Men and Brotherhood Members try to fight them off, but they are too many to contain. While Mr. Sinister is trying to leave however Angel flies out and starts fighting him in the snow. But Sinister is well-prepared and defeats Angel, taking him to a secret Helipad and escaping for good. Inside the Facility scientists are evacuating and Anne Marie manages to absorb Juggernaut's strength and helps fight out, while Pyro and Iceman actually work together with their heat and frost powers. Magneto tells them they need to leave now and everyone evacuates while he pulls down a lot of the structure to crush the current experiments and most of the harmful subjects.
Anne Marie and Remy were both official members of the X-Men and gained the codenames Rogue & Gambit respectively.
Back in New York the X-Men and the Brotherhood are at the Mansion. Where Professor Charles Xavier says Erik is always welcome to help advocate for Mutant Rights in a positive manor like he did with fighting the Essex Corps. Magneto, by contrast tells Professor X he is always welcomed to help him battle against bigots who would see Mutants burn, they shake hands at the end, agreeing to disagree, and going their separate ways. Jean Grey goes to Wolverine and asks him if he has found any peace after he confronted Sinister. He said that he hardly did, knowing all the other Mutants he's experimented on and tortured, only drove him further down the path of wanting to stop that psychopath. Cyclops walks over and says how Wolverine did well in the Essex Corps, and that he can put some of his passion to do good into positive use and help them save Angel from whatever Mr. Sinister is doing to him. Scott and Jean walk off while Wolverine looks envious at the two of them, smitten over Jean Grey. He gets interrupted by Jubilee when she asks him for another round in the Danger Room, he says "you're on" and they go to train.
Inside, Beast tells Professor Xavier that the Mutants who escaped from Mr. Sinister's clutches have literally gone underground, making a home in the sewers and calling themselves the Morlocks since most were given their powers, they don't know how to control them and are using them poorly. Professor Xavier simply goes to his desk and says the X-Men are always ready to help, should they ever need it.
In Alkali Lake, someone is washed up on shore. They quickly put on a mask, and it shows to be Deadpool. Who looks at the camera and says " I'm Back. You didn't think they'd kill me that easily, did you?"
In the Mid-Credits.
In Egypt, deep inside a Pyramid. Mr. Sinister walks up to someone and bows down, saying that their plans to build the most "Evolutionarily sound fighters" had failed and the project completely destroyed, he apologizes for his failure, saying that his own emotions and "getting caught up in the hunt" played a part in their inevitable fate. It is then revealed from the camera the man he is talking to is En Sabah Nur himself, Apocalypse! Who stands up and simply says "Fine, I'll do it myself."
After the Credits, it shows a man walks into a Church and sits down. It stays eerily quiet in the church, as the camera shows the man's face and he says how the ends justify the means. He won't let this world die, before finally saying "I Matthew Murdock, will have to become... the devil."
- Chris Pine as Scott Summers/Cyclops
- Anna Kendrick as Jean Grey
- Jaime Bell as Bobby Drake/Iceman
- Alex Pettyfer as Warren Worthington/Angel
- Adam Baldwin as Hank McCoy/Beast
- Ralph Fiennes as Professor Charles Xavier
- Kelly MacDonald as Moira MacTaggert
- Tom Hardy as Logan/Wolverine
- Naomie Harris as Ororo Monroe/Storm
- Owain Yaoman as Piotr Rasputin/Colossus
- Tyler Posey as Kurt Wagnar/Nightcrawler
- Chloe Bennet as Jubilation Lee/Jubilee
- Matt Bomer as Remy LaBeau/Gambit
- Lyndsy Fonseca as Anne Marie/Rogue
- Zachary Quinto as Nathaniel Essex/Mr. Sinister
- Alexander Skarsgard as Victor Creed/Sabretooth
- Florence Kasumba as Marrow
- Chris Wood as Wade Wilson/Deadpool
- Barbara Palvin as Laura Kinney/X23
- Daniel Day-Lewis as Erik Lensherr/Magneto
- Sienna Miller as Raven Darkholm/Mystique
- Nathan Jones as Cain Marko/Juggernaut
- Riley Smith as St. John Allerdyce/Pyro
- Diane Neal as Valerie Cooper
- Michel Gill as Warren Worthington Sr.
- Peter Macon as En Sabah Nur/Apocalypse (Cameo)
- Patrick J. Adams as Matt Murdock (Cameo)