X-Men II: Deadly Genesis
The X-Men have grown up now and also have two new additions: Havok and Polaris. Angel is reunited with old friend Cameron Hodge, but doesn't realize that Hodge is leader of Weapon X, an organization plotting against mutants. Already aware that Angel is a mutant, Hodge now is certain that the rest of the students at the Xavier Institute are also mutants. Hodge then sends three Sentinels at the X-Mansion where they battle the X-Men. The entire team including Xavier is kidnapped with the exception of Cyclops.
In the subbasement, searching for something to help his teammates, Cyclops accidentally contacts Moira MacTaggert who reveals herself as a mutant scientist as well as Xavier's old friend. Cyclops arrives at Muir Island and explains the situation to Moira and her lover Banshee, with Moira revealing the Cerebro Files. The Cerebro Files were given to her by Charles and include information on every mutant who has been tracked by Cerebro (Cerebro is first introduced in this film). Using these files, Cyclops goes around the world in the Blackbird, tracking down mutants who are mature and experienced with their powers to form the second generation of the X-Men. The new X-Men team includes: Cyclops, Storm, Nightcrawler, Colossus, Rogue, and Thunderbird.
Moira is aware of Weapon X's location as they invited her to come and join them, but she refused as she heard rumors of their anti-mutant plots. The new team travels in the Blackbird to Weapon X and manage to make it into the base. This is all part of Hodge's plan though and he sends brainwashed versions of Havok and Iceman to battle the X-Men. The new team manages to defeat them with difficulty and enters the labs where they meet the mutant psychic Destiny. They also find Angel and Beast however they are both changed: out of spite for his former friend, Hodge amputated Angel's wings while he had Beast experimented on transforming him into a furry ape-like creature. The X-Men are then attacked by brainwashed versions of Jean Grey and Wolverine.
Hodge had earlier placed Jean in a cell with Wolverine who she initially feared. After psi-blasting Wolverine, Jean learned of all the horrors Wolverine had been through thanks to Weapon X and she comforts him, forming a deep bond between the two. Shortly afterwards Hodge had both of them brainwashed to fight against the new X-Men team. Jean's psychic barriers have been broken and she is once more Phoenix, allowing her and Wolverine to overpower the rest of the team. However seeing Scott in danger from Wolverine allows Jean to regain control overherself and she breaks the brainwashing on Wolverine as well as Havok and Iceman.
The team continues on only for Hodge to send Juggernaut after them. Juggernaut is Xavier's half-brother but hates him deeply so he is glad to have a chance to crush Xavier's team. Even with all of the X-Men and Jean's full power, they barely stop him. Rogue then absorbs him and learn's Hodge's plan. Bolivar Trask has created Mastermold, a machine that can create Sentinels much faster than normal but to power Mastermold, the magnetic power of Magneto (and now Polaris as well) must be used. Xavier is being used to power Trask's own version of Cerebro, so he can detect every mutant in the globe, allowing Sentinels to reach them. The X-Men, old and new, rush to the site of Mastermold however learn that Mastermold is already operational.
The X-Men battle Sentinels, guards, and Mastermold while Wolverine finds Trask. Trask only planned to separate humans from mutants, not genocide and tried to rebel against Hodge however Hodge locked Trask up, threatening his family. Trask reveals that Mastermold is well protected but it is secured to a chamber where Magneto and Polaris are, and the chamber is the weak point. Trask believes that by destroying the chamber as well as detonating the base, it can destroy all of the Sentinels and Mastermold but at the price of everyone's lives.
The X-Men are willing to give their lives and use all their powers collectively at the chamber. At the last minute Jean jumps in using her telekinesis to take control of the energies allowing the rest of the X-Men to escape. Trask detonates the base and the collective exposions destroy the entire base as well as all of Mastermold and the Sentinels. As the X-Men regroup outside of the base they see the Phoenix effect, with Jean, Polaris, and Magneto all safe from harm however Jean reveals that Trask is indeed dead as he gave his life to stop what he created.
Hodge however is also alive and tries to escape on a private plane. Thunderbird (who was crippled during the battle with Mastermold) destroys the plan killing both himself and Hodge. As the X-Men mourn his death, Magneto parts ways with Xavier once more, now more determined to make mutants the master race. He is joined by Juggernaut and Polaris (Polaris suspects that Magneto knows of her heritage and that he is her father) while Destiny goes on her own way. The X-Men return home for Thunderbird's funeral where his brother (or the movie counterpart of Warpath) and Thunderbird's tribe comes to pick up his body. Iceman, Havok, Angel, and Beast all leave the team (Angel has no place without his wings now while Beast feels he needs to focus on how to adapt to his further mutation.) Wolverine also wants to leave but Jean tells him that the X-Men is his home now. Wolverine agrees although he mainly does it to stay with Jean, something Cyclops suspects and argues against. This leaves the X-Men team with Cyclops, Phoenix, Storm, Wolverine, Nightcrawler, Colossus, and Rogue. Xavier sees his new team, full of mutants all over the world with different customs and beliefs, making him believe that his dream for peaceful co-existence between humans and mutants is still possible.
In the ending after the credits, Destiny arrives in the altar room of the Hellfire Club's Inner Circle led by Sebastian Shaw (also featuring Emma Frost, Harry Leland, Donald Pierce, and Sunspot.) She reveals that the Inner Circle has long seen the day where the mutant messiah will come and usher in a new age for mutants, one where the Inner Circle rules. Destiny reveals that she has forseen who this mutant is and within the flames of a fireplace, the image of Jean haloed by the Phoenix Raptor is seen with Shaw cackling.