X2: X-Men United

X2: X-Men United (2003) — Colonel William Stryker, the man who put the adamantium on Wolverine, attacks the school and attempts to use a captive Xavier to kill every mutant alive. X-Men and Brotherhood ally. Nightcrawler (Alan Cumming) debuts. Jean Grey dies holding back a flood, and something rises from the water.

Stryker runs a black-site programme on mutants and has a personal stake: his own son is a mutant, and he blames Xavier for it. His weapon is Cerebro — Xavier's telepathic amplifier, which can locate every mutant on Earth and, if the operator wills it, kill them all at once. He builds a duplicate and uses a drugged Xavier to drive it.

Magneto turns the machine's targeting around to kill every human instead, and is stopped. The film ends at Alkali Lake: Jean Grey holds back a flood long enough for the jet to escape, and dies doing it. In the final shot something rises from the water in the shape of a bird. That is the setup The Last Stand pays off.