Professor Xavier and Magneto confront each other for the first time in years, meanwhile Wolverine and Sabretooth come face to face. Professor Xavier tries to examine Sabretooth's mind to figure out his rage problem. After his last terrorist action failed, Magneto plots a new one to bring Professor Xavier out into the open. Sabretooth and Wolverine confront each other in the mansion's war room.
Wolverine has strong feeling for Jean Grey, but she's with Cyclops. Storm has a paralyzing case of claustrophobia and must overcome this as the X-Men venture into the New York sewers to rescue Jean Grey and Cyclops from a deformed race of mutants called the Morlocks. Storm confronts the leader of the Morlocks, Callisto, who wants Cyclops to rule beside her as king.
After leaving the X-Men, Wolverine looks for solitude in the arctic, but comes across Sabretooth, who's been tracking him. When the safety of a local tribe is threatened by Sabretooth, Wolverine must defeat him. Meanwhile Jubilee, Storm and Gambit do some investigating at an island resort called Genosha that seems to be a safe haven for mutants.
Senator Kelly has been abducted by Magneto and given the facts about Magneto's goals of superiority of mutants over humans, the X-men's beliefs of peaceful co-existence between both races, and the Sentinel's plans of global domination. And must make a decision of his future plans in politics based on this information.
Jean and Scott get married. Newly elected President Kelly has freed Beast who has been incarcerated since the attack on government facility at the beginning of Season 1 and added him as part of his Presidential cabinet. Another friend who was thought to be dead at the same incident has resurfaced, but this time he's not so friendly. With the President's newly found pro-mutant point of view, the public feels betrayed are reacting with violence.
Scott and Jean are on their way to a secluded island for their honeymoon, but gets cut short by Mister Sinister. As Morph continues with his plans of revenge against the X-Men, he starts losing his motivation. But Mister Sinister makes sure he finishes what he started. The Friends of Humanity have began to rally.
Storm recovers from her injuries and returns to her duty as leader of the X-Men. When a tear in the astral plane appears in Africa, Storm goes there to investigate. It just so happens that the tear is in her home village. Meanwhile Xavier and Magneto are lured to the Savage Land in Antarctica and Wolverine continues his search for Morph.
Colossus returns home to Russia with Jubilee by his side. They are confronted by a newly revived Russian, life force absorbing, super soldier from the cold war, named Omega Red, who has a bad history with Wolverine. Xavier and Magneto continue their treacherous journey through the Savage Land.
After Wolverine has been lured to Canada by an alleged message from his old friend, Heather Hudson, he finds himself fighting Heather's husband, Vindicator, and the Canadian super team, Alpha Flight, instead. Alpha Flight believes that they were only sent after Wolverine to get him to rejoin their team. However, their General Chasen has a more sinister agenda: to retrieve Wolverine's adamantium skeleton -- at any cost.
Every ten years, The Assassins Guild and The Thieves Guild must each give an offering to a supernatural being called The X-Ternal, in exchange for power. When it comes to be Gambit's brother, Bobby, who has to offer the tithing this time, he comes up missing. The Assassins Guild want to exchange him for Gambit, so he can finally come face to face with the woman he left at the altar 10 years before.