- “Forget everything you think you know. Whatever lessons you learned in school. Whatever your parents taught you. None of that matters. You're not kids anymore. You're not students. You're X-Men.”
The X-Men were a team of mutants created to protect the world as well as maintain peaceful human-mutant relations.
Xavier then brought in Erik Lehnsherr to help lead the team, which also consisted of Havok, Darwin, Beast and Banshee. The team came into conflict with another group of mutants called the Hellfire Club, who were vying for world domination. Following this, Erik and Charles' views regarding the path of the emerging mutant race diverged resulting in the end of their friendship. Erik - now going by the name "Magneto", and Darkholme - now going by the name "Mystique", left the X-Men to form the Brotherhood of Mutants. The group was then disbanded before being reestablished sometime prior to the 21st century.
Sent by Professor X, Cyclops and Storm head North to save two mutants, Wolverine and Rogue, from an attack by a Brotherhood member Sabretooth. He was defeated, and the two mutants are taken to the X-Mansion, where Xavier informs Wolverine of Magneto's plans. Logan decides to stay at the Institute. When Rogue, deceived by a disguised Mystique, leaves the Xavier Institute, Wolverine goes after her, while Cyclops and Storm follow him at the train station. Here, the team battles the Brotherhood, this time led by Magneto himself, who defeats the X-Men and kidnaps Rogue - who was his real objective.Using Senator Kelly's memory, Xavier is now aware of Magneto's real plan: He intends to transfer his powers to Rogue and use her to activate his new machine, which would transform normal humans into mutants. Trying to locate Magneto, Xavier falls into a trap set by Mystique and enters a coma. Jean Grey uses Cerebro, and learns that the Brotherhood is on Liberty Island, wanting to use the machine on the world leaders gathered on nearby Ellis Island.
The X-Men reach Liberty Island and battle the Brotherhood again, during which Wolverine defeats Mystique and Storm kills Toad. The entire team is later imprisoned by Magneto's powers, binding them to the Liberty Statue. Only Wolverine manages to free himself, using his healing factor and stabbing himself in order to break the bindings. After defeating Sabretooth, Wolverine frees the rest of the team and, with the assistance of Cyclops, Storm and Jean, frees Rogue and destroy the machine.
After the mission at Liberty Island, Wolverine leaves the team in order to learn something about his past, following the advice of an awakened Professor X.
After an unsuccessful search at Alkali Lake, Wolverine returns to the Xavier Institute, where he joins once again the X-Men. Following the attempted assassination of the President of the United States, Xavier tracks down the mutant responsible of it, and sends Storm and Jean Grey to take him. The two arrive in an abandoned church, where they find Kurt Wagner, the mutant responsible for the assassination attempt. Wagner seems to have been brainwashed in some way and forced to do what he did by someone else. Meanwhile, Professor X and Cyclops are captured by William Stryker, who, thanks to the information taken with force by Magneto, attacks the X-Mansion and hunts down the students. Wolverine, along with Rogue, Bobby Drake and John Allerdyce, manage to escape the Institute after a brief confrontation with Stryker. The group reaches Drake's place, in which they are attacked by the Boston police - who were tipped off by Bobby's brother. After a fight - in which Pyro almost kills the policemen, the X-Jet arrives and takes them aboard. The plane is soon tracked down and attacked by military forces, which manage to shoot it down. The X-Men are then saved by Magneto, freed from his prison by Mystique. The two members of the Brotherhood offer the remaining X-Men an alliance, since their united powers may have a chance to defeat Stryker's army free Xavier and the other mutants.The two teams start an attack at Alkali Lake base, forcing Stryker to try and escape. While Jean Grey fights a brainwashed Cyclops while Storm and Nightcrawler free the kidnapped students, Magneto reaches Dark Cerebro, in which Xavier is forced by Jason Stryker to kill all the mutants on the planet. Thanks to his helmet, Magneto is immune to both Xavier's mental attack and Jason's illusion manipulation, and reprograms Dark Cerebro so that the humans are eradicated, then leaves. Later on, he confronts Stryker, who's trying to escape the base, and chains him to a rock.
Storm and Nightcrawler then reach Dark Cerebro and manage to stop Mastermind and free Xavier. Meanwhile, after a fight with Lady Deathstrike, Wolverine confronts Stryker and refuses to free him in exchange on information about his past, leaving him chained while the dam is collapsing. Pyro decides to leave the X-Men and to join the Brotherhood, and accompanies Magneto and Mystique on Stryker's chopper.The reunited team returns to the X-Jet, but problems with the engine put them at risk of being killed by the immense water pressure of the collapsing dam. Jean Grey decides to leave the jet and, using her powers, stops the water for a while and makes the jet take off, sacrificing herself in order to save her teammates.
Immediately after the Alkali Lake battle, Xavier and the X-Men reach the White House and talk to the President, who's about to make a speech about the mutant issue. Xavier gives him Stryker's files so that he can see that the assassination was part of Stryker's plan, and warns him that humans and mutants should work together to build peace, or else they'll end up destroying each other in a war.
Cyclops has become depressed over the death of Jean Grey. Beast talks about mutants and the event at Alkali Lake to the public. Logan goes into the Danger Room and sets it on a higher level to avoid thinking of Jean. Iceman saves him by freezing Sabretooth, and Logan sets him up for his Danger Room session. Professor X tells them about the parts at Alkali Lake that they left there, so Wolverine, Nightcrawler, Colossus and Storm go. Missiles start to attack the X-Jet and Nightcrawler teleports in. He goes and opens the doors for his teammates. Colossus and Nightcrawler retrieve the parts, while Storm and Wolverine investigate.Nightcrawler is confronted by Sentinels, while Colossus battles the HYDRA outside. Storm is kidnapped by Lady Deathstrike, and Wolverine attempts to save her. After Lady Deathstrike escapes by helicopter, Wolverine follows.
Wolverine battles many ninjas and eventually finds Lady Deathstrike and Silver Samurai. He defeats Deathstrike and many HYDRA guards, and fights Silver Samurai, who he defeats.
Iceman is sent by Professor X to stop Pyro from destroying a nuclear power plant. Pyro creates a flaming dragon-type creature that Iceman had to fight and prevent him from destroying the power plant.
Nightcrawler and Storm are to the Brooklyn Bridge to stop Multiple Man from destroying it. Nightcrawler disarms the bombs, and both he and Storm take out the clones. During the fight Nightcrawler discovers one of the clones aiming a sniper rifle at Storm at the back of her head. Nightcrawler takes him out, and soon fights the real Multiple Man.
Wolverine informs Professor X that the Mastermold, the machine that manufactures the Sentinels, was in Japan. The X-Men travel to Japan and Iceman fights several Sentinels. Nightcrawler enters the Mastermold and is helped by Jason Stryker. Wolverine battles Sabretooth, and Iceman destroys Mastermold. Jason is now finally free and passes away. Sabretooth is defeated by Wolverine and is trapped in the Mastemold as it was falling apart.
Later on, Nightcrawler informs Professor X and Beast that he did not like the violent life of the X-Men, and decides to leave the team. Professor X states that he is welcome back any time.
By this point, Cyclops has become quite depressed and ignores his duties as both a teacher and a team leader, while Logan tries to act as his substitute. Worthington Labs announces that a "Cure" for mutants has been developed, which prompts ex-team member Dr. Hank McCoy (aka "Beast") to return to the X-Mansion and discuss the situation with his old mentor, Xavier.
Caught up in his grief, Cyclops leaves the Mansion alone and returns to Alkali Lake where, in rage, he blasts the water. Hitting the lake, surprisingly, he awakes Jean - who protected herself with a telekinetic cocoon. The "old" Jean has been replaced by her murderous and almost all-powerful persona Phoenix, who seemingly kills Scott. Feeling the disappearance of Scott's mind from his perception, Xavier sends Storm and Wolverine to investigate. The two find Jean unconscious and take her back to the Institute, where it becomes clear that the Phoenix is now dominant: after knocking Wolverine unconscious, Jean leaves the Mansion and returns to her childhood home.
Worried about her potentially unlimited powers, Xavier, accompanied by Storm and Logan, reach the Grey family home, but discover that Magneto too has been acknowledged of Jean's resurrection, and wants to make her join his newly reformed Brotherhood. While Xavier and Magneto confront Jean - both trying to recruit her into their respective camps, a battle occurs outside the house: Storm easily defeats Arclight and Quill, but is beaten by Callisto, while Wolverine is vanquished by the Juggernaut. During the battle, Jean becomes enraged and kills Xavier, almost destroying the whole house in the process. While Logan and Storm mourn their mentor's death, Magneto takes Jean with him and leaves.After the deaths of Xavier and Cyclops, Storm takes the lead of the X-Men, and decides to battle the Brotherhood, who plans to destroy Worthington Labs and stop the "Cure". The team is joined by Beast and some of the students (Iceman, Shadowcat and Colossus). Arriving on Alcatraz Island, where the labs are located, the team joins the army stationed there in the fight against the Brotherhood: Storm finally kills Callisto, while Angel manages to save his father from the Omegas and Kitty stops the Juggernaut from killing Leech, the young mutant whose DNA is the source of the "Cure". After a brief fight, Wolverine, Beast and Colossus manage to defeat Magneto and inject him with the "Cure", depowering him. When the battle seems to be won, Phoenix becomes enraged and starts destroying everything around her - buildings, vehicles and people. While everyone escapes, only Wolverine manages to go near her due to his healing factor and, after declaring his love for her, kills her.
After the Alcatraz battle, there is generally greater cooperation between humans and mutants. Beast leaves the X-Men and becomes the new US ambassador to the United Nations, while Storm becomes the new headmistress of the Xavier Institute. During the Post-credits, Charles manages to transfer his consciousness into his twin's body before his old one was disintegrated by the Phoenix.
In an apocalyptic future, most of the mutants and humans have been killed by the unstoppable Sentinels and the remaining X-Men are scattered. Due to the threat, even Magneto has allied with his former enemies. In this future, using Cerebro, the few surviving X-Men and the Free Mutants unite to try to change time by using Shadowcat's powers to project Professor X's mind back to 1973 to stop Mystique from killing Bolivar Trask and starting the chain of events that led to this dark future. As Shadowcat can only send someone safely back a month before their mind is destroyed, including Professor X, the X-Men send Wolverine back instead as his healing powers will allow him to survive. While Wolverine attempts to change the past, the X-Men are forced to defend the monastery they are hiding out at from a massive Sentinel attack to buy Wolverine the time he needs. All the X-Men fall until only a mortally wounded Magneto, Professor X, Shadowcat and the time-traveling Wolverine are left. With no choice, Shadowcat cuts the connection keeping Wolverine in the past and the apocalyptic future is erased due to Wolverine's actions in 1973. In the new future, the X-Men once more exist as they previously had as does the Xavier Institute which is again run by Professor X. Wolverine's changes to the timeline have seemingly affected more of the X-Men's past than just the Sentinel program as both Jean Grey and Cyclops are shown to be alive as well.
In 1983, 10 years after Wolverine altered the timeline, Charles and Hank reopened The Xavier School for Gifted Youngster where they took in many students including Jean Grey and Jubilation Lee. Sometime later Alex Summers brought his younger brother Scott so he could receive help in controlling his powers. Later at night, Jean has a nightmare about the end of the world after calming her, Xavier and McCoy decide to investigate and learn that an earthquake occurred in Cairo, Egypt that coincided with Jean's nightmare. The next day Charles and Alex travel to Washington D.C so that they can learn more about what happened from Moira who was also present in Cairo investigating a group of followers who believe in an ancient mutant of great powers. That same day, Raven returns to the mansion and brings along Kurt Wagner whom she had rescued and tells Charles that Erik has resurfaced after his family was killed by police. Using Cerebro Xavier manages to locate Magneto and finds out he has joined Apocalypse and his Horsemen. Apocalypse then proceeds to take control of Xavier through Cerebro to make all the Earths governments launch their nuclear missiles into space. In a desperate attempt to cut the connection Charles tells Alex to destroy Cerebro.
Apocalypse and his Horsemen then arrive and kidnap a unconscious Xavier. Alex tries to stop them by firing a energy blast but misses and ends up hitting the X-Jets fuselage which causes an explosion. While Peter Maximoff is able to get everyone to safety Alex who was the closest to the blast range is killed. William Styker then arrives and captures Raven, Hank, Moira and Peter.
Jean, Scott, and Kurt sneak aboard and free a experimented on Logan who proceeds to slaughter most of the soldiers before finally being calmed down and having Jean restore his memories before he finally escapes the facility. Freeing the others the group travel to Cairo with a Jet stored in the facility and dawn flight suits, determined to stop Apocalypse plans.
On the way a nervous Jean ask Raven if she was scared on that fateful day in Washington D.C. in 1973. Raven says no but tells them that she was scared on her first mission and fondly recounts the heroic efforts of her allies. Arriving in Cairo Jean discovers Apocalyspe plan is to transfer his mind into Xavier which would allow him to control everyone. The group splits up as Raven and Peter go to stop Erik and the others go to rescue Charles. Nightcrawler teleports into the pyramid where he is attacked by Archangel. After a grueling battle Nightcrawler manages to defeat Archangel and rescue Charles before the mind transference process can be completed but not before Xavier loses all of his hair.
Meanwhile Mystique and Quicksilver locate Magneto. Raven proceeds to tell Erik that while he thinks he has lost all his family tells him that he still has Charles, herself, and Peter who does not directly tell him that he is his son. On board the Jet the others attempt to escape with Xavier only for Psylocke and Archangel to send the jet crashing but Nightcrawler is able to teleport everyone to safety. Apocalypse calls out Charles only to be attacked by both Quicksilver and Mystique who he subdues and tortures to call out Charles. Xavier reminded that through the mind transference process he and Apocalypse are still connected enters Apocalypse mind and proceeds to brutally beat Apocalypse. However, Apocalypse gains the upper hand and proceeds to brutally thrash Xavier. Meanwhile, Cyclops and Beast try to hold off Apocalypse physical body and are aided by a reformed Magneto. However, Apocalypse still proves to be too powerful and advances until Jean having unlocked the power of the Phoenix comes and changes the tide and proceeds to burn away Apocalypse armor and body. Apocalypse tries to escape but Storm then also comes to their aid as Jean fully vaporizes Apocalypse.
In the aftermath, Xavier and Moira rekindle their relationship. Erik and Jean help reconstruct the school, but Erik refuses Xavier's offer to stay and help teach. Hank, Scott, Jean, Ororo, Kurt, Peter, and Raven become the new X-Men, and Hank and Raven train the new recruits for the battles ahead.
Despite their best efforts and helping him defeat Ajax, Colossus and Negasonic Teenage Warhead were unable to convince Deadpool into joining the X-Men. Although Deadpool did promise that, in return for Colossus and Negasonic Teenage Warhead helping him defeat Ajax, he would think about joining the X-Men.
Some time in 2028, an aging Xavier's mental instability led to a seizure, during which he lost control of his powers and let out an involuntary psychic attack. In the attack he experienced in Westchester, the location of the X-Mansion, he harmed 600 people, and killed seven mutants, including several members of the X-Men. By 2029, the X-Men had been disbanded with the only known members alive being Xavier and Logan, the latter of whom was resilient enough to survive Charles's seizures and became his caregiver alongside fellow mutant, Caliban.
Also by 2029, no new birth of mutants had occurred in 25 years while old mutants were persecuted, hunted and forced to hide. However, the adventures of the X-Men over the years were also documented and published into comics for the large public.
- There are some characters from the comics who was planned to be included in the movie team but didn't make it:
- Beast in X-Men and the second movie (he was added only in X-Men: The Last Stand).
- Gambit in X-Men: The Last Stand (appeared in X-Men Origins: Wolverine as a loner).
- Nightcrawler in X-Men; The Last Stand (Alan Cumming declined since he suffered from the prosthetics in the previous movie and didn't want to do that again for a minimal role).
- Angel in X2: X-Men United (appeared in X-Men: The Last Stand).
- Emma Frost in X-Men: The Last Stand (she was added in X-Men: First Class and appeared as a villain).
- Jubilee in X-Men: Days of Future Past (now appearing in X-Men: Apocalypse but still not as a member of the team).