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At Finland at the Weapon X facility  the guards were chasing someone.Turned out that a mutant nicknamed Nightcrawler escaped and they want him back.Using his ability to teleport, Nightcrawler quickly managed to take down a guard and took his snowmobile.At Dr.Cornelius' command, the guard opened fire on the mutant and by shooting his shoulder they stopped him. John Wraith arrived and ordered his men to take the mutant in custody and torture him for this unwanted behavior, than took out a cigarette and began smoking while we saw that there was the S.H.I.E.L.D. logo on his uniform.
   Wolverine was in Arizona to search for the remains of the Weapon X with the help of Professor Charles Xavier and told him that what he went through with the program left him more of the beast than human in him. 

Back to the X Mansion, Jean explained Hank that the serum they gave him to save his life not also changed his hair but gave him more  psychical strength  as well, but when asked how she really feels about Wolverine, Jean told Hank that no matter how Wolverine 'redeemed' himself by taking out Magneto, she will never be able to trust him again. 

In Japan,Tokyo the X-Men were guests at a reality show but the only members who were there were Cyclops, Storm and Colossus.They explained that they are not a threat to the World and they only want to make the globe a better place and they do believe in that the human and mutants one day would live in peace with each other.During their way out they gave the crowd signatures and while Colossus wasn't paying attention, a hooded girl from the crowd appeared and touched Colossus' skin making him a but pale as they went home with the Black Bird. 

Back to Finland, John Wraith is being updated by the girl who touched Colossus and turned out to be non other than Rogue
who is also a solider in the Weapon X and by taking all of Colossus' memories with the touch John Wraith is in possession of all of their secrets including their School for Gifted Children and they can take them down once and for all.

Not much later, Wolverine and Cyclops took down a root of the Russian mob who were menacing Colossus' family and during their way back to the mansion, Wolverine explained Cyclops that he really changed thanks to Prof. X and he will leave to search for those who destroyed his life. 

Back to the mansion everybody is having a good time, Storm and Beast were having a picnic which ended by the two kissing, Bobby Drake is back from his vacation and Jean is feeling a bit guilty for telling to 'go to hell'. 

That night, the mansion was attacked by the Weapon X.The team Sabretooth, Juggernaut, Nightcrawler and Rogue took down the team and imprisoned them.The only problem was that they haven't found Wolverine.
Meanwhile in Delhi, Nick Fury is searching for the weapon X as well when he was attacked, he took them down really fast but something arrived and his men lost contact with him. 

At the Weapon X facility, John Wraith was talking to his bosses and told them that the X-Men are now part of his S.H.I.E.L.D. team.
 At their cells later, Cyclops told Juggernaut that he already has three escape plans and once the president of the United States finds out that they kidnapped them, they will come and take the whole program down. 

At Nightcrawler's mind, Jean is having a conversation with the mutant and told him that everything's going to be just alright.
At the time Beast was transformed into a blue skinned mutant thanks to the experiments Dr.Cornelius was making on him.
     Next morning the newly assigned S.H.I.E.L.D. team was sent on a mission to rescue Colonel Fury but before they started, Sabretooth informed him that if they're planning everything fancy the nanobots in their heads will be activated to blow their brains out. 

At the laboratory, John Wraith is desperate to find Wolverine so he began using Cerebro.

The X-Men team successfully saved Fury but with a great cost.Jean had to kill someone in order to have the mission done. 
Back at their cells, Bobby lost faith but Colossus told him that Wolverine will come and save them.Sabretooth arrived and told them to stop believing in 'angels' because they've just captured Wolverine at St. Petersburg.  

In a flashback it turned out that Wolverine and Fury go way back and Wolverine once saved him and since then they were like friends. 

In New York, Fury is thinking about saving the X-Men from John Wraith after an annonymus source he got informed.
" Abracadabra..."

At the Weapon X facility in Finland, Jean apologized to Wolverine about what she said earlier but Wolverine told her that they haven't 'captured' him because it was just all part of a bigger plan to get them out of there. 

When John's bosses ordered him to shut down the facility, John killed them while Wolverine was dragged out by Sabretooth to show him the files which contained Wolverine's life before the Weapon X and burned it all in front of Wolverine than they shoot him and Sabretooth began torturing him by telling him that he was the one who killed Wolverine's wife and kid.Suddenly all lights go out as the X-Men realize that they are being rescued by non other than the Brotherhood: Quicksilver, Scarlet Witch, Blob, Mastermind and Toad

Thanks to Vanda's power, the nanobots were removed from their brains and there's nothing now to hold them back from escaping.
At to woods Wolverine is now battling an upgraded Sabretooth who now has bigger fangs and four adamantium claws in each hands.The two began fighting and Wolverine ends up victorious. 

Thanks to the Brotherhood the X-Men escape and John Wraith is killed by Colonel Nick Fury who after that took over the S.H.I.E.L.D. and became the 'boss'. 

Back to the X Mansion, Professor X confessed Jean that he didn't kill Magneto but brainwashed him and made people to believe that he was really dead. 

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