Havok and Polaris

Later, Havok, with Polaris again, joined the second incarnation of X-Factor, a newly formed, government-funded, mutant agency. They overcame Ricochet and Mister Sinister's attempts to discredit the team. They fought the Mutant Liberation Front and the Hell's Belles. They took down X-Force after an assassination attempt was made on the life of Charles Xavier. During a mission to Genosha, the connection between Havok and Wolfsbane was discovered.

The team battled the fanatical terrorist Haven, who believed that, when the Mahapralaya came, the world would be destroyed and a new golden age would come about after it. Haven hoped to bring Mahapralaya about early. She took Wolfsbane through a Pralaya, moving her in and out of pocket dimensions, and cured her of the genetic bond. When Haven tried to cure Multiple Man of the Legacy Virus, she failed, killing him. Havok was deeply affected by the apparent death of his teammate and friend. Mourning Jamie's death, he decided to quit the team until Polaris tracked him down and convinced him to stay with the team.