In the sewers, Wolverine is chasing Sabretooth. He pauses in front of three
tunnels, thinking which one to choose. Then he sees a shadow in one of them
and runs inside. A man looks after him. His goggle view screen shows a
silhouette of Wolverine with the word 'mutant'. On the radio, Bolivar Trask
tells the Shadow Team to "take the lead." Three soldiers go after him. Again
they reach three tunnels, and each takes one. With an X-Ray laser, one of
them sees Wolverine behind the bricks. Wolverine seems to notice one of the
soldiers, but prefers to chase Sabretooth. The soldier says that he's
chasing another mutant. There's a cut to Sabretooth, he's looking for
Wolverine. He is crawling in a small tunnel. Once he gets out, Wolverine
jumps on him and they begin to battle. Suddenly, a grate falls and wraps
itself around Logan, trapping him. It seems to be the work of Magneto. The
soldiers decide to use this chance to capture him. He slashes his way out
and runs after Sabretooth, but the soldiers capture him in some sort of
green goo, and Sabretooth runs away. Bolivar Trask and some soldiers appear.
One of the soldiers tells Trask that the other mutant escaped. They cannot
track him down because of some sort of a magnetic interference. Trask
replies by telling them to call off the search.

At the mansion, Jean is using Cerebro. She informs Professor X that they
lost Logan's signal. He tells her to keep trying, but she says that he
disappeared, and so did Sabretooth. He gets angry, slams his fist on the
keyboard and tells her that this way they will never be able to find
Magneto. Jean gets very upset, apologizes, and says that she is not ready for
this yet, but Xavier calms her down, telling her that it is not really her
fault. They continue to search.

Back in the sewer system, Storm and Beast are looking for Wolverine. They
can't find anything, and Hank doesn't understand how anyone could take
Wolverine without him slashing something. Then they find a wrecked grate
that looks as if it was handled by both Wolverine and Magneto. An owl
watches them leave and flies away.

The owl flies to the Brotherhood house and reveals itself to be Mystique.
Quicksilver and Blob are playing cards, Toad is watching television and
Avalanche is lying on the couch. Mystique tells them that Magneto kidnapped
Wolverine, just as the Scarlet Witch enters. Lance does not understand why he
would do that, and Mystique answers that neither does she. She asks
Quicksilver about Magneto's location. Pietro answers that he has no idea
about his father's whereabouts. Mystique says that Magneto must be planning
something big, and that he forced her to make her move.

The day passes, and in the mansion, the X-Men and the New Mutants are in a
session in the Danger Room. They are not doing too well. Rogue and Sunspot
just got tagged, and they join the other tagged kids outside. Rogue sits
next to Berzerker and comments on how hard the session is. Iceman tells her
that at least she lasted longer than he did. Back inside, the enemy is
Magneto. Nightcrawler tries to save Magma from being tagged, but gets
tagged himself. Magma joins Cyclops, Jean, Spyke and Shadowcat and tells
them that Kurt was tagged. Spyke is amazed by how many kids were already
tagged. Cyclops asks Magma about the objective, and she answers 36
kilometers, while she really meant meters. Orange paintballs start shooting
around. Scott pulls Amara away and Evan hides behind a rock. A paintball hit
a rock above Amara, but Scott saves her with an optic blast. Professor X
yells at Cyclops to make a move or turn over a command to Jean, because
Magneto won't just sit around waiting for him to make a decision. Scott
makes a decision to rush Magneto. Jean levitates to Magneto's left while
Scott uses his optic blasts to clear the path and get to his right. Kitty
phases Amara through the ground. Amara fires her hands. Evan accidentally
makes a rock tumble and hit Magneto. His helmet falls, and he explodes.
Everybody try to run away, but then paintballs hit all of them. Xavier uses
a microphone to call everybody to the planning room angrily.

In the planning room, Xavier is very angry with the X-Men and yells at
Cyclops, telling him that Magneto can never be taken by surprise. Scott asks
him why he is acting this way. The professor answers him that he was trying
to check whether they were ready to battle Magneto or not, and they are
clearly not. Scott says he thinks they are ready. Xavier answers that they
will not even be ready to face the Brotherhood, that the New Mutants aren't at
all ready, and that he has no choice but to refresh the line-up of the
X-Men. The Brotherhood walks in, and Xavier tells the X-Men to welcome their
new teammates. The X-Men are angry and do not understand why they have to
join forces with the Brotherhood. Evan asks them why they want to join
anyway. Pietro answers that they have their reasons. Lance says that they
obviously need a new team leader, and Scott angrily says that he can have
the job, before leaving. Jean wants to go talk to him, but Professor X tells
her to let him go, as they have to go continue the search on Cerebro. He
tells the X-Men and the Brotherhood to go train in the Danger Room.

Wolverine and Trask arrive in a place that looks like a military base in a
truck. Wolverine tries to release himself, but Trask electrifies him. They
go into an elevator and Trask reveals that while he was working with SHIELD
he learned about mutants and that he thinks that they're a menace that
poisons the gene pool. Logan tries to convince him that some mutants are
good, but Trask continues and says that someone has to do something to
ensure the survival of the human species, and that Wolverine is needed to
assist him in an experiment.

In Cerebro, Jean finally finds Logan just as Xavier enters. Professor X
orders her to gather the teams. Beast, Shadowcat and the Brotherhood board
the jet and get ready to leave as Mystique is in the control room, messing
with the defense system. She sets it on self-destruct and starts it on
Defcon 4. Back in the hanger, on the other jet are Professor X, Storm,
Spyke, Rogue and Nightcrawler. Ororo and Xavier are having an argument over
should they wait for Scott or not. Xavier claims that if he lost his
confidence than he will only be a liability. Storm says that it is a mistake
and that they need him. Eventually, they leave without him.

Right as the jet leaves, the mansion defenses lock up. Bobby and Sam run
downstairs but cannot get out. The only one who succeeds to get out in time
is Amara. Sam tries shooting himself at the door, but he's too late and it's
already covered and locked. Outside, the mansion's defense systems try to
hit Amara. Tabitha arrives in Lance's jeep, bombs the gates and helps Amara
escape, and they hurry away as Tabitha blows off the guns. They drive and
meet with Scott, who is alone, thinking about earlier, and tell him what
happened. He gasps and says "DEFCON4", and the three of them drive back to
the mansion in Scott's car. On the way, Boom-Boom tells Cyclops that she was
on her way to tell Professor X that Mystique is in charge of the Brotherhood
again, and he adds that up to the defense systems going crazy and to the
Brotherhood's joining the X-Men, figuring something isn't right.

In the military base, Bolivar Trask introduces Wolverine to a Sentinel, a
huge robot he created, a weapon designed to destroy all mutant life forms.
The Sentinel attacks Logan but Wolverine runs away. He then tries to slash
the robot's wires, but fails, to Trask's enjoyment. The Sentinel throws
Logan away. Wolverine tries climbing the wall to escape, but the Sentinel
shoots again and knocks him unconscious.

Cyclops, Magma and Boom-Boom arrive at the mansion through the waterfall.
Inside, Sam tries to shoot himself to break out, but it fails. The guns aim
at them. The countdown to the self-destruction begins, showing ten minutes
left.

Meanwhile, in the piers, five travel spheres show up from the air and land.
Out of them come the Acolytes – Sabretooth, Pyro, Gambit, Colossus and
Magneto.

Back in the military base, the Sentinel is picking up Wolverine.
The Sentinel prepares to fire.