The X-Tinction Agenda was a nine-part crossover event (or X-Over, as X-Men crossovers are sometimes called) beginning in 1990 that took place in the pages of Uncanny X-Men, The New Mutants, and X-Factor. Chris Claremont and Louise Simonson were the principle writers, while star artists Jim Lee, Rob Liefeld and Jon Bogdanove illustrated.
Cameron Hodge, now a cyborg, sends his Magistrates, lead by a brainwashed Havok, to attack the X-Mansion. They capture several members of the X-Men and New Mutants, namely Storm, Wolfsbane, Boom Boom, and Rictor. They also kill Warlock. After becoming mutates, Storm and Wolfsbane end up brainwashed like Havok. Mutates, like the three of them, are slaves on the island nation of Genosha and dominated by an elite human minority similar to apartheid. Several mutant groups from around the world gather and travel to Genosha in order to rescue their friends. They include the remaining New Mutants lead by Cable, X-Factor, and X-Men members previously scattered across the globe.
Once in Genosha, many of them end up captured as well, including Wolverine and Gambit. Cyclops manages to reach Havok, and helps his brother overcome his brainwashing. At the opportune moment, Havok turns on his master, Cameron Hodge, enabling others to revolt as well. Cameron Hodge is beheaded and then buried alive by Rictor, who also causes the Genoshan capital building (known as the Citadel) to collapse onto Hodge's remains. In the wake of the battle, Havok and Wolfsbane decide to stay in Genosha in order to help rebuild the country and protect the mutant population.
Storm was programmed by the Genegineer to snap out of her mutate state with the ability to restore a mutant's power by touch. This is first manifested when she restores Cyclops's power after the trial. A side effect of coming out of her mutate condition was that Storm once again possessed an adult body and could control her powers more fully. Also, the rest of the X-Men get to see the new Betsy Braddock. Havok stays in Genosha so as to help rebuild the country and to see that the mutates are dealt with in a humane way.
During the events of the X-Tinction Agenda, Wolverine lay dying in a cell. Jean Grey had been placed in this cell as well and the two shared a moment of intimacy. This scene further showed the confusion Jean feels concerning the emotional bond she has with both Wolverine and Cyclops. Cyclops is shown to acknowledge that his hold on Jean is strained, at best, and tried to rein her in during some key elements of various battles. Jean showed that she still had a mind of her own and could help in whatever way would be best for the teams.
The team most influenced by the events of the X-Tinction Agenda. In an attempt to rescue his friends, Warlock de-powered their cell and allowed himself to be captured. This ultimately led to Cameron Hodge trying to assimilate the transmode virus, which would allow him to shift his shape. Rahne stopped the process but it was too late for Warlock. He became the only one to die at during these events. His ashes would later be spread on Doug Ramsey's grave.
In trying to stop Hodge from taking Warlock's power, Rahne herself was captured and turned into Mutate 20. Even after Storm touched her, if Rahne stayed in her human form she would still be a mindless mutate since her suit was bonded to her. She did, however, gain even more power in her wolf form. The Genegineer explained that all Rahne's former inhibitions were taken away and her mutant powers would evidence this. True to form, Rahne's lycanthropic form was far more fierce and difficult to calm. Rahne decided to leave the New Mutants and stay in Genosha to help with its rebuilding process.
X-Men: X-Tinction Agenda Trade (2001)
Essential X-Men #10