At a café in Bayville, Logan is reading the newspaper about Apocalypse's
dome in Mexico. Bobby, Jamie and Ray are sitting with him, doing nothing. He
asks them if they don't have anything better to do, like their first day in
class with Scott and Jean. The kids complain that Scott and Jean have
totally nerded out - becoming instructors has affected their brains. They
even named their training session: "The Application of Physics within the
Strategic Use of Mutant Powers". Bobby begs Logan to come lead the session
instead, but Logan answers that if Scott and Jean have something to teach
them, it might be a good idea to learn it, and goes to his motorcycle.
Suddenly, he senses something in the air, and starts walking into an alley.
He turns around and sees his foe's coat on a rooftop, but then metal
tentacles come out of the wall behind him, trap him, put a weird device on
his forehead and take him.

In the Institute, Scott and Jean are heading for their first training
session as instructors. Scott is worried that the kids would rather be
outside training than inside studying, and Jean tells him to relax and that
she likes the idea of teaching the New Mutants the science behind using
their powers. They enter the classroom and find, to their shock, the New
Mutants fooling around, shooting at each other. Fireballs and electricity
bolts shoot all around. Sam fires outside, knocking Scott over.

Wolverine wakes up ties to the floor with a collar, hands cuffed. He pops
his claws and slices the chain, and then makes a hole in the wall, but finds
out that he's in a jet flying high in the air. The door opens, and two
soldiers fire at him. He falls out of the jet to the air onto a tree, down a
hill, off a cliff and into a lake. Two ropes come down from the jet, and
down them slide Gauntlet and Omega Red. Gauntlet was the man with the coat
earlier, and Omega Red was the one with the tentacles. They look around, and
start walking. Wolverine gets out of the lake and walks a little, and then
dodges a red beam sent by Gauntlet. He falls from a small cliff and hides
inside a hollow log, waiting for his healing factor to kick in. The metal
tentacles find him and pull him up again. Omega Red calls Wolverine Weapon X
and says that he's been waiting a long time for this. Wolverine asks if he
knows him, and Omega Red tells him that his games won't save him this time –
this time, Wolverine will be the one left broken to suffer. Gauntlet tells
him to be patient, since they have a job to do. Suddenly, X23 jumps at Omega
Red, knocking him over, and slices the tentacles. Gauntlet tries firing at
her, but she dodges and kicks him, knocking him down. She jumps over to
Wolverine and tells him to get up. Omega Red and Gauntlet slowly get up, and
Gauntlet reports to HYDRA command that the target has arrived – X23 is in
play. X23 puts her foot on Wolverine, pops her claws and asks him why he's
there. He tells her he's just as surprised to see her and asks what's going
on. She retracts her claws, gets her foot off, sniffs the air and tells him
he has to get out of there. He asks what about her, and they start walking
through the woods.

A while later, Wolverine is still behind X23 as they walk through the woods.
She tells him that he should have been healed by now, and he tells her to
give him a break – he started the morning by falling off an airplane. She
says that he's slowing her down, and he says that he isn't as young as he
used to be and thanks her for her concern. Nearby, Gauntlet and Omega Red
are tracking them. Wolverine tells X23 that he looked everywhere for her
that night and asks why she left the Institute, as he could have protected
her. She is surprised, saying that she left to protect him – if she hadn't
left, HYDRA would have taken him and his friends too – HYDRA will never let
her go, and neither will SHIELD – they want her to use her. Suddenly, they
both sense Gauntlet and Omega Red coming. Wolverine doesn't understand how
they could find them, but X23 finds the answer immediately – there was a
tracking device in Wolverine's boot. She angrily tells him to just get out
of there before he gets caught, but he says he's not leaving her out there.
She explains to him that they set him up - they knew she was there and that
she would find him – she's the one they want, not him. Gauntlet realizes
that they found the tracer and says that they'll have to do it the hard way.

At the Institute, Scott and Jean are trying to teach the New Mutants, who
are not paying attention at all. Amara is talking to Roberto, Bobby is in
his ice form, and Sam throws a paper ball at Jamie, making him duplicate.
Scott starts handing out papers, as Jean tries explaining to the kids that
this is really important because physics, geometry and math impact directly
on using their powers. Sam drops his paper, and Amara burns hers. Scott
gives her another one and asks if anyone else needs one, and a bunch of
Jamie(s) raise their hands, to the kids' amusement. Jean angrily tells the
kids that they all need to take this seriously - Scott and she are their
instructors now. Everybody get quiet as Jean sighs and says that at least
Bobby is paying attention. Everybody giggle as Jean thanks Bobby, when
suddenly he falls and breaks – he was just a statue of ice. The kids burst
in laughter and immediately volunteer to go look for Bobby, and run out of
class. Scott tells Jean to cheer up – they'll get through to the kids.

Wolverine is finally healed, and he and X23 and sniffing and listening,
trying to hear the villains. Nearby, Omega Red sees something in a bush, but
it's only a bear. Gauntlet stands on a cliff and locates Wolverine on a
tree, sniffing around. Wolverine tells X23 that they're being pushed
somewhere – it's a trap and they're walking right into it. She tells him he
doesn't know what he's talking about, and he tells her it's called
experience. She tells him he's wrong, and he asks her to trust him and let
him help her. She answers that no one can help her - the only way she'll be
free, the only way HYDRA and SHIELD will stop hunting her is if she's no
longer alive. He says that they both have been through the same kind of
things, and even though they took his memories away, he's proof that she can
get beyond this. She wishes they'd take her memories away and tells Logan
that if he really wants to help her he should stop following her. He decides
to follow anyway.

A short while later, they are walking in a narrow valley between cliffs.
Wolverine again says that it looks like a trap, and she apologizes. Guns
start firing at them, and they hide behind a rock. It doesn't work, as
soldiers surround them all around, including on the cliffs. X23 jumps at
Gauntlet, and he fires with a sonic wave, and X23 and Wolverine cover their
ears until they fall unconscious.

In the HYDRA facility, a woman welcomes the ties Wolverine to HYDRA, calling
him Weapon X. Omega Red is standing beside them. Logan asks where the girl
is, and the woman answers that she's where she should be - within HYDRA, the
people who own her. He asks why they can't just leave her alone, and she
answers that she's the one hunting them - she's been on a crusade to find
and destroy every one of their bases. They've set traps for her, but she's
always managed to evade them until now. Now that they have her back, they
can finish what they started after they'll wipe that rebellious mind of hers
clean. When they're done with her, X23 will be the perfect weapon she was
designed to be - one without emotion or free will. Omega Red asks what about
Wolverine and the woman answers that Weapon X is last year's model. He's
all his as per their agreement.

In a nearby lab, a doctor looks at the tied X23, and sees that she has a
disc on her forehead. He angrily tells himself that he told Gauntlet not to
use the disk - it could interfere with the mind wipe.

Omega Red tells Logan that he deserves it – him and all of his Weapon X
comrades. Logan tells him that he doesn't know what he's talking about or
who he is, but Omega Red just continues, saying that he will have his
vengeance - Wolverine is only the first - Sabretooth, Raid, Maverick – they
will all pay. He then uses his tentacles to throw the chair, but it hits the
controls, and the electric sparks release Logan. Wolverine easily defeats
Omega Red and runs out.

In the lab, the doctor is on the phone with Gauntlet. Gauntlet tells him he
didn't use the disc, and the doctor realizes, a second too late, that X23 is
awake.

In the hall, Wolverine notices that the defense system is sliced, and
soldiers fly out of a room. X23 enters the hall from the room, and Logan
tells her they have to get out of there. She refuses, saying that this is
exactly the place she's been trying to get into - the supreme HYDRA is there
– she did this to her. Logan is shocked to realize that she got caught on
purpose, and she tells him that it's him who shouldn't be there. Omega Red
shows up, and he and Wolverine start battling. X23 runs the opposite way,
attaching mines to the walls and telling Logan to get out – he doesn't have
much time.

The woman from before, Madame Hydra, enters the control room, and the guy
there tells her X23 has escaped and suggests she returns to the command
ship.

In the hall, Wolverine manages to trick Omega Red and stuck his tentacle in
a control panel, electrocuting him. The computer sends a warning that
explosive devices have been detected, and one of the mines goes off as
Wolverine runs.

In the command ship, Madame Hydra rushes to the controls. The ship takes
off. X23 is outside, climbing on it. Wolverine runs out just in time to jump
on the ship too, and X23 yells at him to let her go. He tells her that it
doesn't have to be this way, but she says that it does and kicks him off the
ship. She enters the ship and tells Madame Hydra that that she did it to her
– she made her a monster, a weapon. Madame Hydra begs for mercy, and then
Gauntlet enters and tells X23 that it's over. She tells him he's right, and
throws mines all over the ship.

Wolverine gets up and watches as the ship explodes and falls to the ground.
Later, SHIELD agents are leading Omega Red into a helicopter. Nick Fury
walks up to Logan and asks him where the girl is. Logan says she didn't make
it. Later, they get on a helicopter. Before entering, Logan sniffs the air
and smiles – X23 is sitting on a rock, now free at last.

In the Institute, the New Mutants are in the classroom, this time sitting
quietly. Bobby tells Scott and Jean that he's practically an X-Man – he
doesn't need to learn this stuff – none of them does. Scott and Jean explain
that they understand that they aren't that much older, but they have been
doing this for longer, and they've learned a lot since they've been there
working with the professor, Storm and Logan – they've got experience. To
demonstrate, Jean lifts all the students in the air, and Scott puts an apple
on Bobby's desk and fires an optic beam that bounces on all walls and gets
exactly to the apple, cutting it. The students are all indeed very
impressed, and Jean lowers them back. Wolverine watches and smiles to
himself.