In Westport, Connecticut, two young mutant children
run for their lives, their parents having just been killed. Their pursuers,
called the Purifiers, quickly catch up to them in a playground and callously
gun the children down before displaying their dead bodies with the word
“Muties” on the playground swings. All for the crime of being born mutants.
Some time later, the children’s bodies are found by Magneto, who swears that no
more shall die and that the ones responsible will pay! In New York City, fanatical
Reverend William Stryker works on a sermon before reviewing briefing tapes on
the X-Men and their powers, all while planning something sinister. We then cut
to Stevie Hunter’s dance studio, where Kitty Pryde is in the middle of a fight
with a boy named Danny. Colossus soon arrives to break up the fight and
Stevie Hunter demands explanations from both. Danny said he supports the Stryker
Crusade, who have plans to save humanity from mutants, which Kitty obviously
took issue with, leading to the fight. Kitty runs off in frustration, while all
the while the X-Men are being surveilled by the Purifiers.
Back at the mansion, the X-Men all sit down to watch a
televised debate between Charles Xavier and Stryker. Stryker continues with his
rhetoric of the dangers of mutants, rarely giving Xavier time to rebuff. After
the debate, and Stryker’s ominous notions of treating mutants as if they aren’t
human, the X-Men get ready for a Danger Room session to blow off steam, each
with their own thoughts and worries. The X-Men are tasked with protecting a
family of mannequins while transporting a large block to the other side of the
room, each with their own individual goals. They complete their objective by
switching goals and using teamwork to get the block to the other side and end
the session. Meanwhile, in Central Park, the Purifiers attack Xavier’s car and
he, Cyclops, and Storm are apparently killed! Back at the mansion, the X-Men
are just finishing up their Danger Room session, when Nightcrawler answers the
phone to hear that there was an accident and that Professor Xavier, Scott, and
Ororo are dead!
The next day, Kitty sulks on the grounds of the
mansion, being comforted by Illyana Rasputin, neither able to believe their
friends are dead. As they walk the grounds, they find a strange sensor and
Kitty phases through it, before hiding to see who comes to fix it. Meanwhile,
the others investigate the site of the “accident.” Wolverine determines that it
was only made to look like an accident and that the burned bodies that were
found are not Xavier, Scott, and Ororo. They then spot the Purifiers watching in
a car across the street and take them by surprise. The X-Men are then surprised
themselves when two of the Purifiers reveal powerful mechsuits, but they are
immediately dispatched with the arrival of Magneto, who announces he’s there as
a friend and ally. Back at the mansion, another group of Purifiers arrive to
fix the sensor they set up and Illyana is captured. Kitty attempts to tail them
by phasing into the trunk of their car, but they release a dose of nerve gas
into the trunk to knock out Kitty as well.
Just the Purifiers leave, Magneto and the X-Men
return. Magneto tortures the Purifiers they captured for information and learns
that they plan to use Xavier to bring about the extermination of mutants!
Elsewhere, Xavier is plagued by visions of being crucified and tortured by the
X-Men, revealed to be part of Stryker’s plan to break him, suspending Xavier in
an isolation tank and drugging him in order to bend Xavier to his will. Cyclops
and Storm, also being tortured, which feeds into Xavier’s visions, ask Stryker
why he’s doing this. Stryker thinks back to thirty years previous, when he was
an Army Sergeant. He and his pregnant wife were traveling when they got into an
accident, and she was forced to give birth. Stryker was horrified at the
appearance of his mutant son and killed both his newborn child and wife in
shame. He attempted to kill himself too by putting them all in the car and
lighting a match, but Stryker was blown clear of the car. After drifting for
awhile in despair and anger, he came across an article on mutants written by
Xavier and believed that mutants were the work of the devil and that it was his
calling to save humanity from them, in the name of God.
After Stryker gives the order to kill Kitty, the
Purifiers pull over but find that Kitty has escaped the trunk. Kitty runs but
she finds herself in the midst of a street gang, where the head Purifier, Anne,
quickly finds as well. Anne is forced to kill the gang, while Kitty slips away
in the confusion, eventually able to find a phone to call the mansion. The
Purifiers chase Kitty onto the El train and shoot a cop who tries to protect
her. The train suddenly lifts into the air, signaling the arrival of Magneto,
while the other X-Men quickly deal with the Purifiers. Meanwhile, Stryker’s
brainwashing of Xavier appears to be complete when Xavier apparently kills
Cyclops and Storm after an order from Stryker. Not long after, Kitty captures
Dr. Ramsey, the man who was overseeing Xavier’s brainwashing and Nightcrawler
intimidates the man for information. Some time later, Scott and Ororo’s bodies,
along with Illyana, are loaded into an elevator at the Stryker building, before
Magneto lifts the entire elevator out of the building, while Stryker’s
right-hand woman Anne narrowly manages to escape. Wolverine determines that
Scott and Ororo aren’t dead and Magneto revives them, determining that Charles
must have unconsciously held back and merely put them in stasis.
Later that night, Stryker makes the final preparations
for the big sermon he’s giving at Madison Square Garden. Stryker sets up Xavier
to scan for all nearby mutants and kill them when he makes contact with them.
Stryker begins his sermon, detailing that any deviation from how God made
humanity, i.e mutants, is of the devil and needs to be exterminated for the
good of the future of mankind. Meanwhile, Xavier’s mindscan is put into action
with the X-Men and all other nearby mutants feeling the effects. Magneto
arrives to confront Stryker directly and Stryker turns Xavier’s power directly
at Magneto full force. It knocks Magneto for a loop, making him realize just how much
Xavier had been holding back before, as Magneto is barely able to keep the
angry crowd back. The police and many of the spectators are beginning to see
the insane extent of Stryker’s views. While Magneto confronts Stryker directly,
the X-Men sneak in the back and deal with the Purifiers in an attempt to get to
Xavier.
Anne runs to warn Stryker, when she suddenly feels the
effects of Xavier’s scan, revealing that she’s unknowingly a mutant as well!
Stryker rebukes her and pushes her from the stage, where she falls to her
death, all caught on live TV. Backstage, the X-Men pull a clever move to
incapacitate Xavier. Nightcrawler teleports with Wolverine right behind Xavier,
who blasts them away, while Cyclops ricochets his beam off of multiple surfaces
to nail the distracted Xavier. Though they seem to have won, the X-Men instead
head onstage to confront Stryker directly. Cyclops debates with Stryker, saying
that they’re just as human as everyone else, regardless of what they can do.
Stryker points to Nightcrawler, indignant that they would dare call him human
and Kitty fires back, saying he’s one of the kindest, most human people she
knows and that she’ll stand with him over believing in Stryker’s supposed God.
Stryker pulls a gun on the X-Men but before he can fire, he’s shot by one of
the cops and taken into custody.
Back at the mansion, Xavier feels lost and despondent
over everything that happened, nearly ready to agree to Magneto’s more violent
methods for his mutant utopia. Cyclops steps up and convinces Xavier to take up
his dream once more. Even though it will be hard, the means are just as
important as the ends, built on the hope of a better world. Xavier once again
rejects Magneto’s offer, to his disappointment. Kitty offers Magneto to join
their cause, but he declines, not able to fight for something he doesn’t
believe in. Magneto departs, genuinely hoping the X-Men’s way succeeds, but if
it doesn’t, then it’ll be his turn. Xavier is overcome with gratitude at
Scott’s empowering words, and Storm echoes the sentiment, proud at how Scott
handled both confronting Stryker and convincing Xavier that his dream was still
good. Scott just says that he helped someone in need, which is what it’s all
really about, what makes the world go ‘round. So they’ll continue to fight for
a world where that’s so.