X-Men: The Last Stand (2006)
The human government develops a cure for mutations, and Jean Gray becomes a darker uncontrollable persona called the Phoenix who allies with Magneto, causing escalation into an all-out battle for the X-Men.
When a "cure" is created, which apparently can turn any mutant into a "normal" human being, there is outrage amongst the mutant community. While some mutants do like the idea of a "cure", including Rogue, many mutants find that there shouldn't be a "cure". Magneto, who still believes a war is coming, recruits a large team of mutants to take down Warren Worthington II and his "cure". Might seem easy for the X-Men to stop, but Magneto has a big advantage, which Wolverine doesn't have. Jean Grey has returned, and joined with Magneto. The Dark Phoenix has woken within her, which has the ability to destroy anything in her way, even if that "anything" is an X-Man.