Storyline
Professor X asks the X-Men to return to Alkali Lake to retrieve irreplaceable parts to Cerebro. Nightcrawler is asked to infiltrate the remnants of William Stryker's base with his teleportation ability, since the weapons systems were somehow operational. Once inside, he finds out that Stryker had a backup plan to destroy the mutants...mutant-hunting robots called Sentinels. Working together, Storm and Wolverine find an A.I. module for a Sentinel when agents of HYDRA (an organization of terrorists) arrive to take the remaining Sentinels to their own base. It is revealed that HYDRA had designed the robots for Stryker. Inside the base, Wolverine discovers that HYDRA had employed one of his former adversaries Lady Deathstrike (who was able to survive an apparent death in X2 after being pumped full of adamantium).
Nightcrawler and Colossus destroy the generators for Alkali Lake. Nightcrawler is then plagued by visions of a youthful, angry Jason Stryker who continues to remind Nightcrawler that he left him to die. It is revealed that Jason Stryker is alive and well and wants to continue his father's dream of seeing all mutants destroyed. Jason escapes with agents of HYDRA and the Master Mold. Storm and Wolverine then battle Lady Deathstrike until Lady Deathstrike eventually escapes the facility with the remnants of HYDRA as well as the remaining Sentinels and the Master Mold. Wolverine tells Storm he is going to follow HYDRA. He promises to return as he hitches a ride on Lady Deathstrike's Tokyo-bound helicopter. Iceman, Storm, Colossus, and Nightcrawler return to the Institute.
Iceman is told to fight Pyro, who is threatening to destroy a nuclear reactor. After a battle, Pyro escapes and Iceman meets up with the rest of the team after Xavier praises his skills in the battle. Nightcrawler and Storm face off against one man who is many: Multiple Man. Nightcrawler defeats Multiple Man who is sent to a prison for high-powered mutant criminals (this storyline is somewhat picked up in X-Men: The Last Stand, when Magneto and his new Brotherhood free Multiple Man from the Prison Convoy).
Jason activates the Master Mold in Tokyo, causing the Sentinels to be activated. They begin to hunt down mutants, capturing them, and Iceman sets out to prevent this from happening, and destroys many of the Sentinels.
Wolverine infiltrates HYDRA's main base and cuts through many of their forces. As the Silver Samurai consults Deathstrike about her feelings of dishonor, Wolverine interrupts their discussion. Yuriko announces she'll handle Logan, and the Silver Samurai exits the Dojo. A battle ensues, ending with Wolverine slicing a rope suspending a large wooden platform; the large structure breaks through the floorboards, taking Yukiro with it. Wolverine then tracks the Silver Samurai to the roof of the facility. Silver Samurai reveals that he is himself a mutant, and if Wolverine is able to honorably defeat him in combat he will tell Wolverine how to defeat the Sentinels through the Master Mold. Conquering Samurai in combat, Wolverine gains the information, and tells the team how to defeat Master Mold.
Xavier telepathically contacts Magneto, and asks him for help in facing the Sentinel forces. Magneto agrees to a final team-up saying the next time, it will be as foes again. The X-Men are attacked by new, towering Giant Sentinels leaving Iceman to defeat the robots. Iceman wipes out these Sentinels as Master Mold lurks in the distance. Magneto arrives and uses his powers of magnetism to crush the many Sentinels attacking the mutants. The temporary alliance over as Magneto sends Sabretooth after a new recruit for his Brotherhood: Jason Stryker.
Arriving inside the Master Mold, Nightcrawler must disable its control center while he is aided by a kindly apparition of Jason Stryker, who helps point the way through the maze of the Mold's body. When he arrives at the Master Mold's command center, he finds Jason, who hates the younger "ghost" Jason, a manifestation of his split psyche. Wolverine arrives in the Master Mold, and Jason uses his powers to make Wolverine fight himself in a mental battle in the Weapon X Lab, to fight his own demons. Wolverine is victorious against a horde of himself, and he heads to the Master Mold's head. Jason tries to get rid of Nightcrawler by entering his mind and trying to convince Kurt that he is not a mutant, but a real demon. Nightcrawler disables the Master Mold's neural net, changed by Jason to look like a demonic realm. Meanwhile, Iceman destroys the core of the Master Mold.
Sabretooth works his way to Wolverine and Nightcrawler's location, knocking Nightcrawler out and taking the wheelchair bound Jason, when Wolverine arrives and attacks his nemesis. The two have a vicious battle, ending with Logan throwing Sabretooth from a great height to be impaled below. Jason dies in the battle, the good part of his psyche winning, and tells Nightcrawler it is okay for him to leave him this time.
With the Sentinels, Master Mold, and Jason out of the picture, the X-Men head home. Nightcrawler tells Xavier he does not want to be an X-Man, for their lives are too violent and he is a peaceful man. Xavier tells him he is always welcome in the Mansion, and Kurt leaves (which explains his absence in X-Men: The Last Stand).
Read more about this topic: X-Men: The Official Game