Bolivar Trask finished building the Sentinels and set out to hunt down mutants as he claimed that they are a global threat. Killing the first mutants, all details went online and another broadcast reported that Magneto and his Brotherhood of Mutants declared war against the 'homo sapiens'.Meanwhile in San Diego Hank after a bar incident is recruited by a girl called Jean Grey.After that Jean also recruits Ororo Munroe and Piotr Rasputin. Once they all found themselves in Wenchester county at a school owned by Professor Charles Xavier who founded the building for gifted youngsters as he calls it.They first met Scott Summers aka. Cyclops who gave them uniforms and codnames so the Sentinels could not detect them.Ororo became Storm, Hank Beast and Piotr Colossus. After the introduction, Prof. Xavier told them that Erik Lansher once was his friend who betrayed him and became Magneto.Not much later Xavier used a special device nicknamed Cerebro to located another mutants, Bobby Drake. The young Drake was in NYC, Time Square chased by six Sentinels and the X-Men, how they called themselves, defeated all five giving the final shot to Bobby who destroyed the last one of the robots.Although ended up victorious, the people didn't liked them and they had no other option but to flee.
Elsewhere at a place called Savage Land, Magneto and his brotherhood, Toad, Quicksilver and Scarlet Witch are talking about Xavier and finally Magneto reveals his plan that he sent someone after Xavier. The perfect killing machine who is non other that Wolverine.
Perhaps a week later, Logan arrived at the JFK Airport where a guy called only as John Doe was waiting for him and was amazed how he managed to walk through the metal detector, but Logan responded in only one sentence "I'm professional". As soon as they both were in open area, John was killed and Wolverine captured by unknown persons.Meanwhile the X-Men is on their way to help and recruit Wolverine because as the prof. said , it's better to have him on their side than vica versa.Logan woke up on an adamantium cell only to realize that his attacker was non other than John Wraith, the one who "made" him. After torturing him,the X-Men arrived and saved Logan who wanted to kill ultimately John for what he did, but Jean managed to calm him down. Wolverine than joined the X-Men.At the savage land, Quicksilver and Vanda are suspicious about this and Magneto revealed that he was the one who informed the Weapon X about Logan so things can look more real when the X-Men arrive.
Days later, Bobby,Peter and Ororo are out shopping when a bunch of Sentinels arrived to arrest mutants and thanks to their uniform, their mutant DNA is hidden so they look normal. Same time, Wolverine is training in the Danger Room where he managed to kill all the X-Men members.After the training Jean and Prof. X both tried to read Logan's mind but with no success due Logan's weapon X training which helped him keep his thought blocked.Cyclops although didn't trust him, he allowed him to go with them on a mission to Croatia to save the president's daughter who have been kidnapped by the Brotherhood and Magneto.
Arriving there they managed to save the girl and bring her home successuly but that almost cost Beast's life.Quicksilver was
although hurt by Logan and told Magneto who arrived and let the X-Men go for an unknown reason, that maybe Logan turned on them but Magneto assured his son that if he's late it's only because Logan first wants to sleep with a girl from the team.
Back at the X Mansion, Jean tried out a new serum on Beast which turned his hair blue and than went to a walk with Logan at the rose garden where she told Logan that he doesn't trusts her and suddenly they started making out where Cyclops saw them. Scott than became jealous and left the mansion.He went to the savage land where Magneto was standing and told him that he was right and he came to join the Brotherhood. Magneto greeted him as 'brother Cyclops'.
Same midnight, the Brotherhood now with Cyclops in command caused havoc in London killing many people. Cyclops didn't kept a secret he disagrees with the way the brotherhood took this "warning message". At Washington DC at a hotel room, Wolverine and Jean are talking about Cyclops whom Logan calls a bastard for betraying them and after that they have sex.
Also in Washington DC, the X-Men now with a recovered Hank, Xavier talks to the President who is grateful for saving his daughter and in return he will close the Sentinel project but before that happens,the Sentinels still have one more mission, to hunt down and kills Magneto and everyone at the savage land.
The Sentinels quickly arrived to the savage land and attacked and killed many mutants.Magneto did not tolerated this and with his magnetic power re-programmed the sentinels whom now where hunting people with human gen and headed to Washington to end this once and for all by killing the President of the United States. Cyclops than managed to get Quicksilver and Scarlet Witch on his side and called Professor X to inform him that they have a ''little problem".
The invasion began and Magneto now with an army of Sentinels attacked the White House and the whole Washington and the X-Men began fighting them while Professor X warned telepathically the people of the city to get out from there.
Meantime, Jean and Wolverine are fighting.Jean telekinetically throw Wolverine to the wall after founding out that Wolverine entered the team only to kill the professor for Magneto. Wolverine told Jean that he confessed this because now he is on their side and will stop Magneto.
At the White House, the President is naked on the ground while Magneto holds the flag of the United States of America and told the people that today is the day when homo sapiens fall and homo superior will take control of Earth. Magneto then tries to murder the president when Professor X arrived and the two began fighting telekinetically.Wolverine showed up and proved to be on the X-Men's side stabbing several times Magneto with his adamantium claws. Magneto managed to hit Wolverine with an iron piece and tried to bring down the White House while Logan was lying on the ground unconscious. Not knowing how to stop him, Quicksilver took his father's helmet which stopped Xavier from entering Magneto's mind with his giving an opportunity to end this once and for all. Now being on his old friend's mind, Charles Xavier doubled his friend's power transforming him into an electric force field summoning everything that's made of metal to 'him' with this causing a big explosion above Washington apparantely killing Magneto.
Back to the Xavier Institute for Gifted Children, Xavier is having a conversation with Cyclops and told him that no matter what he did he is proud of him because ultimately he choose the good side in this fight and in the end that is only what matters. When asking what will happen to Wolverine, Xavier told Scott that like him, Wolverine proved them that he is fighting the good fight too and next they he will help Logan tracking down John Wraith and those who made him Wolverine the way he is and erased his memory at the Weapon X project. Outside Cyclops and Charles sit down for a champagne and Xavier told Scott that this was only plan one and the second one will be much more interesting...