A screen with headshots of mutants. The pictures get scrolled through until it reaches a picture of Logan and stops, bringing up his information. The person operating the computer is wearing a black uniform with a mask with two eye controls that look like red lights. The person looks at Logan's photo and touches the screen, then angrily extends 2 claws on one hand and slashes the computer screen and others around it. Alarms instantly sound signalling an intruder. The intruder runs past a guard who has been knocked out. He has a circular object on his forhead with a red glowing light on it. A pair of guards see a group of walls that the intruder has sliced through. The intruder runs to the roof, followed by two guards with guard dogs. The intruder reaches the edge of the roof and as the person turns to face the dogs two claws extend on both hands. A helicopter tracks the intruder in its beams, but the intruder slices through a pipe causing mist to cover everthing. The person zips past the guard dogs and flips over, digging claws into the side of the building all the way down to the bottom. Helicopters shine lights on the building and see the claw marks. The helicopters scan the parking lot but don't see anyone. The person is seen in the sewer moving away.

Outside of the Institute a training session is going on. Iceman and Berzerker are walking through the woods and they hear rustling in the leaves from where the intruder is watching them. Berzerker complains that he doesn't understand why Logan can't have them train in the Danger Room. Iceman makes claws on one hand out of ice and mimics Logan by saying "There's no off switch in the real world, bub." The two laugh, but then Berzerker falls into a concealed pit. Bars immediately close him in. Guns start shooting paint balls at Iceman, who says he'll come back for Berzerker. Iceman ices up and ices his way past Sunspot and Multiple who are hanging from a tree with dupes below trying to reach them. He tells them he'll come back for them also. He also passes Cannonball who is trying to blast out from under a net with no luck. He tells him that he'll also help him later, and that he'll never learn anything if he has to keep rescuing them. He runs into Logan and falls down and when Logan hauls him up by his shirt Iceman asks him if he won. Logan says all of them are going to have to do the course again. Two helicopters fly overhead and Logan asks Beast to take over for him. With that news the students cheer, but Logan warns them that he'll be watching.

In the infirmary Professor X tells Rogue that she seems to be fully recovered and that she can rejoin the others. She tells him that she needs a little more time, and he tells her she can take as much time as she needs. As he leaves he wonders if her response had anything to do with Logan's training session and she pretends that she didn't know it was that day.Outside Professor X asks Logan why Nick Fury thinks that he had anything to do with the SHIELD break in. Logan says he doesn't know, but that if Fury thought he really didn't have anything to do with it, he wouldn't be picking him up with armed guards. The guards escort Logan on to the helicopter and Fury and the Professor exchange looks, although neither say anything.

At SHIELD headquarters Logan examines a section of wall that has been cut out. Fury tells him that the intruder not only had metal claws, but also had his DNA. Fury tells him that he needs Logan's help to find out what's going on. They enter a room with more armed guards where a blonde woman stands. Seeing Logan she says "Weapon X!" and he bristles, causing the guards to ready their guns. Fury tells them to all calm down. The woman tells them they haven't much time, but Fury tells her to start from the beginning. She introduces herself as Dr. Deborah Rizman and tells them she worked for Hydra. Fury says that they're a spy organization. She admits that one of their operatives was sent to infiltrate their building, but that the person went rogue. She tells them this is cause for concern, and proceeds to show them a video. As the video loads Logan asks her why she worked for "the bad guys" and she explains that it gave her the chance to push genetics beyond what any government would allow. She tells them that she was trying to create "the perfect weapon" and that Hydra had acquired data from the Weapon X program. While she speaks the video shows the masked figure seen before in a training sequence, leaping around a room and completely taking out a group of huge robots. Dr. Rizman had failed 22 times, but the 23rd worked because they realized they needed Logan's healing factor. Logan asks incredulously that they cloned him, but Dr. Rizman tells him that she had had to add some genetic variation. However, in breeding out emotion they inadvertently added instability, including "explosive anger". On the video X23, having finished with the robots, slices open a wall into a room where the scientists are, and begins to hack at machinery causing the recorded video footage to end. Dr. Rizman tells them that X23 is out there, and that she must be found.

Back at the mansion X23 is watching Beast's training session. Multiple and then Beast swing over a ditch on a rope. Then Multiple and his dupes pile up on Beast. X23 watches and recalls a training session in the pouring rain with bags of sand thrown at her as she slices through each one. Her accuracy is perfect but the session doesn't let up, and eventually she misses one and is knocked to the ground. Remembering where she is X23 turns to watch Iceman who shoots rings of ice for Cannonball to fly through. Sunspot, who has tied back a tree, lets it go and thwacks Cannonball with the tree which completely falls. X23 looks angry and extends her claws. Beast arrives blowing his whistle and tells them that that'll be it for the day. The girl sheathes her claws while Multiple and Sunspot laugh at Cannonball and leave.

Dr. Rizman tells Logan and Nick Fury that Hydra completely molded the girl from birth. We see a baby basket in a metal room crying alone, and then a young girl climbing on a horizontal metal pole across a huge chasm. Dr. Rizman explains that she could have left, but she stayed for the girl's sake. She tells them that although they trained her to blend in with others, when she saw loving families she became hostile. We see a girl opening a music box next to X23 on a park bench, and then X23 being led away, as Rizman looks at the smashed remains of the box still on the bench. Rizman tells them at 12 she was put through the Weapon X process. At this Logan explodes and Rizman sadly says that she's here because she wants to help try to undo some of the damage she caused.

At the Institute Weapon X watches the students from outside. She sees Bobby and Sam playing chess, Ororo watering her plants, and Kitty on the phone and Kurt teasing her. She remembers shivering, stuck in a completely white, empty room and growls. She sees Scott and Jean washing and drying the dishes, and Jean using her power to squirt water at home. Professor X is moving down a hallway when he senses Logan. He turns around when he hears the sound of a girl crying. He sees X23 at the chessboard and moves towards her. She suddenly hits him with one of the neural inhibitors, and he falls to the ground.

On the way to a helicopter Fury tells Logan that the last files the girl looked at were about the X-Men. Dr. Rizman tells Fury that his agents can't handle X23, and he tells Logan he has an hour before his agents come in. Meanwhile, X23 is exploring people's bedrooms in the mansion. She is an Jean's room looking at her photographs when Sam walks in, and she quickly takes him out with an inhibitor, punching him through a wall. Bobby walks down the hall wondering what the noises are and enters Kurt's room. On the floor he sees Jean, Kitty, and Kurt and he turns around just in time to get nabbed by X23.

Ray and Scott enter the study and see the Professor on the ground. Ray says he saw the same thing on Amara. Just then they hear someone trying the door. They get on both sides and prepare to take out whoever is trying to enter. But it turns out to be Rogue, who they quickly let in. Ray and Scott explain the situation and Ray prepares to zap the inhibitor off of the Professor's forehead. Logan enters and quickly explains that they're wired to explode. He wants to get the three of them out, but they refuse. They enter a room and see Ororo and Roberto on the ground. Ray exclaims that not even Logan could take them all out, to which Logan just snarls. In the library they see dupes of Jamie and Beast. A section of the floor under Logan gets sliced away and he falls. X23 jumps up into the room and dodges Ray and Scott. She takes out all three of them and knocks Logan to the ground. In a large room he yells at her to talk to him. She throws a marble bust at him, then hits him with a chunk sliced out of a column. The fight continues, and X23 knocks Logan around, almost hitting him with a bookcase, a piano, and a huge chandelier. He tells her that noone should've had to go through what she went through, and she's a child even though they tried to take that away from her. She struggles out of his grip and knocks him out of the front door, surprising him with a claw from her foot. When he asks her why she came after them, she said it wasn't them, it was him and that it was his fault. When Logan tells her he had nothing to do with it she says he's lying and continues to attack her. Eventually Logan knocks her to the ground. He tells her that they were both victims and that he's the only one who can understand her, and the closest thing to family. By now X23 is in tears, and she steps forward into Logan's arms who comforts her. Helicopters with searchlights appear, causing X23 to back away. Logan tells her to get away, and she runs. Fury lands and Logan says that he has to let her go, and then walks back to the mansion.

The next day Rogue is by a window. The Professor and Logan enter and Logan tells her that he wants her for a training session, and tells her she'll like this one. Outside the New Mutants are with Storm and Beast. Everyone sighs when they see Wolverine approaching with a bag. Wolverine tells them that today they'll be doing: mutant dodgeball, and extra points for anyone who takes out Iceman. Professor X asks him why the change, and Wolverine says that "Sometimes you've gotta let kids just be kids." The two of them smile as they watch the New Mutants cream gang up on Iceman.