Full story
The movie opens with two flashbacks. In 1986, Charles Xavier and Erik Lehnsherr visit young Jean Grey's home together to invite her to the school. Ten years later, young Warren Worthington III tries to cut off his own wings in the bathroom, and his father learns his son is a mutant.
In the present, Warren Worthington II's company announces a "cure" for the mutant gene, derived from a boy named Jimmy, aka Leech, who cancels the powers of anyone near him. The news splits the mutant community. Rogue, who can't touch anyone, seriously considers taking it. Magneto gathers a new Brotherhood and promises war. When a convoy tries to haul Mystique away, he frees her, but she takes a cure dart meant for him, loses her powers and gets left behind. Later, she tells the government where Magneto is hiding.
Cyclops, still a wreck, goes back to Alkali Lake and finds Jean alive. She kisses him and he vanishes. Wolverine and Storm bring her back unconscious to the mansion, and Xavier explains that years ago he locked away a second personality inside her, the Phoenix, with almost limitless power. Jean wakes up, runs to her family's house, and both Magneto and Xavier show up there. The Phoenix takes over and disintegrates the Professor in front of everyone. Jean leaves with the Brotherhood.
Without their mentor, the X-Men regroup under Storm, with Beast back on the team. Magneto attacks Alcatraz Island, home of the cure facility. He rips the Golden Gate Bridge loose to make a path to the island. The X-Men hold the line, Beast hits Magneto with cure darts and he loses his powers. Jean, out of control, starts tearing everything around her apart. Only Logan can reach her, healing with every step. In one last moment of clarity, Jean asks him to save her, and Logan kills her with his claws.
In the end, Storm runs the school, Beast becomes a UN ambassador and Rogue comes back cured to Bobby. In a park, Magneto, alone, makes a metal chess piece wobble: the cure might not be permanent. After the credits, Moira MacTaggert checks on a coma patient, and he greets her in Xavier's voice. That thread is left open.