Episode 1. Things pretty much start just like the trailer. The team before the break is Cyclops, Jean Grey, Storm, Shadowcat, Iceman, Colossus, Beast, Nightcrawler, Rogue, and Wolverine. The mansion is destroyed. Jean and Professor X are "missing". The mansion is destroyed and the X-men disband and go their separate ways. A year later, the X-men are still disbanded, and the institute mansion is still rubble. Hank stays behind in the labs trying to figure out what happened to Xavier. According to his analysis, Magneto did not do it, but that's all he can figure out. An anti-mutant police force called the MRD are policing mutants in NY and locking them up. Senator Kelly is also trying to put forth a mutant registration act.
After Wolverine helps a family whose daughter was nearly caught in an explosion, he's burned and taken in by them while he's healing. A friend of the family figures out that Wolverine is a mutant and reports it to the MRD. Wolverine escapes, but the family is taken by the MRD. So Wolverine and Beast hijack an MRD truck and rescue the family, and Wolverine incapacitates John Wraith, who looks to be the head of the MRD. Wolverine puts the family in a place to lie low for a while and decides he and Beast need to reform the X-men since the MRD are going too far. That's the first episode.
Episode 2. The Brotherhood which includes Quicksilver, Domino, Blob, and Avalanche, and Toad are terrorizing the city and are going after Senator Kelly. Kelly has enabled a new MRD weapon, a Sentinel Prowler robot that goes after an incognito Rogue at his press conference. Wolverine and Beast stop it, after Angel fails to help Rogue escape. Wolverine asks Angel and Rogue to rejoin them. Angel says he can't since his father supports Senator Kelly even though he knows that Warren is a mutant. Since Angel uses his father's money to help support mutants in secret, if the information went public, he would be cut off. Rogue refuses to rejoin the X-men. She's noticeably angry at Logan who doesn't understand why she's upset. Earlier in the first episode, Wolverine was preparing to take a temporary leave, which Rogue wasn't happy about either since she feels that Logan is her only connection to the institute. It feels like they are trying to hint that Rogue has a thing for Logan, but Logan can't look at her as anything except a friend or a little sister.
Wolverine and Beast search for the other members. Iceman went back to live with his parents. Colossus went back to Russia and refused Beast's invitation to return, not wanting to leave his family. Kitty went missing but is heading to Genosha. Magneto currently rules over Genosha, and there are billboards around advertising it as a safe, protected paradise for mutants. Wolverine and Beast get back Iceman, and then Kitty. Wolverine tries to bring a broken Cyclops back who refuses. Wolverine then taunts Scott who simply blasts him away.
The Brotherhood instead tries to recruit Rogue. Domino is able to talk her into it. The Brotherhood then comes up with a plan to initiate Rogue after they annihilate Senator Kelly's house, and Rogue then absorbs Warren's father to find out where Kelly will be. Rogue then goes to the X-men and says she wants to join them now, and leads them to the press conference to stop the Brotherhood. The Brotherhood sets off an explosion at the press conference and the ceiling starts to collapse. The X-men intervene to help, but the MRD goes after them. They get into a big fight and escape, and Rogue is now nowhere to be found. After Warren saw her leave, Wolverine realizes that Rogue played them and hung them out to dry. Rogue returns successfully to the Brotherhood and it looks like she has thrown her lot in with them for now.
The mansion and institute are being rebuilt with money from Warren. Wolverine doesn't want to talk to Rogue anymore. I think at the end, Emma Frost comes to the school, and she can find Professor Xavier.
Episode 3. Emma Frost wants to join the rebuilding X-men. Wolverine is very suspicious of her since she founded her own school for Mutants in Michigan, but says "she only taught them how to bully people". Emma says she has had a change of heart and wants to be a part of a team for good and can use Cerebro to help find Xavier, and Wolverine thinks she just wants to get her hands on it. But since they need a telepath he allows it. Forge who is now a young man has joined the team as their tech, and has been repairing the danger room, black bird, and cerebro. Emma uses Cerebro and finds Xavier alive in Genosha.
Wolverine goes to Cyclops again and convinces him to come back since they found Xavier. He leads the team of Beast, Emma, Kitty, Cyclops, Forge, and Iceman to Genosha to find the Professor. Wolverine's angry since he believes Xavier in Genosha means that Magneto blew up the mansion and kidnapped Xavier. Beast doesn't think that is necessarily so, but Wolverine wants to rush in guns blazing without trying to contact Magneto. Cyclops asks Emma about Jean, since she Jean was not found in Genosha through Cerebro. Emma plants some tension by implying that she can find Jean, but Wolverine wants her gone ASAP. It looks like she is trying to play Cyclops.
The X-men barely make it into Magneto's island undetected since repairs are being completed on the blackbird as they are flying. They land in Magneto's Citadel which is a huge metal castle. The team splits up to look for Xavier.
Magneto shows up and kicks EVERYONE's ass. He uses Wolverine's metal skeleton against him and tries to force Wolverine's claws into Emma and Beast. Wolverine apologizes and beseeches Magneto to stop which he does at the sight of Wolverine's humility. He shows them the Professor who showed up on his island a week earlier. Emma says Xavier is in a deep coma and has no brain activity. Wolverine asks he be taken back, and Magneto instead tells the X-men they can make Genosha their home. Wolverine refuses, but Magneto leaves the offer on the table. The X-men return back to the mansion with the unconscious Xavier. Soon afterward, they see an astral projection from Xavier, who is speaking to them 20 years later in the future. Xavier says the team disbanded and fell apart, and the future has become a grim and terrible place. He says in order to prepare for what's coming they must remain a team, and Wolverine must lead them. This ticks Cyclops off and he tries to leave, but Xavier says they cannot win without him so Cyclops decides to stay for now.
After Xavier's future image departs, we flash forward and see that it was in fact Xavier from the future. He flees from the ruins of the institute after using Cerebro. And he's walking with bionic leg bracers. He passes by gravestones all located on the mansion's grounds. All of which have the names of the X-men. The future is a burning war ground much like Days of the Future Past and the Sentinels have taken over.
Back in the present, Wolverine says they have to get over their issues and remain united because the world needs the X-men. End of pilot.