Back at The Brotherhood, they are riding on a subway train.
Pierro is upset about Magneto's death and he's furious that the X-Men stood by and did nothing to help him.
Lance tries to talk to him and tell him that Magneto wasn't the loving father he remembered, that he really hated him. Peitro freaks out and his powers go haywire and derail the train.
At Bayville High, Scott and Kitty see the flames, "What's that, a fire?" He thought.
"It's a subway accident, people are trapped there," Kitty said. "Let's go if we can help," Lance said, and both head over to help.
Meanwhile, the Brotherhood are trapped in the subway car with no exit.
Pietro tells Fred to make them a door and Fred takes off running, knocking holes through the train as he goes. The rest of the Brotherhood follow him.
Lance hesitates as they pass some of the other passengers, "Come on, we are going to get out of here," He tells the passengers.
The firemen and rescue workers arrive and the subway starts to explode. Lance and the lady he's carrying barely escape ahead of the explosion.
The media jump all over the story, calling the Brotherhood heroes. The X-Kids stand by speechless.
On television, Principal Kelly has a campaign commercial airing where he's running for mayor, "Hello, I am Kelly. Do you feel safe everyday mutant moves freely through our city, our street, and here through our school."
"And they are powerful. I am going to register for every single one of them. These creatures must be marked, because trust me mutants are animals."
Kelly is running on a strict anti-mutant platform, calling for registration of all mutants.
The commercial is interrupted with breaking news of the Brotherhood heroics. Kelly is not happy with this.
—
At the Xavier Institute, Kitty put a newspaper in front of Scott, and she asked him, "Can you believe this?"
Scott denies it, because they know the Brotherhood only saves themselves, not the others, but Xavier tells them they need to give them a little chance.
—
Back at the Brotherhood house, when they found out saving someone can give them money, they started doing it many times, and they themselves created the situation before saving them.
Pietro talks them into doing one more rescue, something big so they can go out with a bang. He sabotages a train and it loses all control.
When the Brotherhood show up to save the day they find out that the train is now on a collision course with another train, one that is pulling eight tankers of gasoline.
Pietro says he'll see them outside of the blast zone and speeds away. Toad and Blob pile into Lance's jeep and take off.
Lance stays behind.
Xavier shows up to get the X-Men. He tells them, "The Brotherhood is going too far and that they've created a crisis situation. The authorities can't do anything and have asked for their help."
Kurt, Scott, and Kitty phase onto the train, they lead the conductor to the second car and Scott blasts the connector and frees the rest of the cars from the engine.
Jean is able to stop the first train and races to the second train engine to try to stop it, Kitty is seated on the top of the engine.
Kurt teleports on the train where Kitty is seated, "What are you doing?" He asked her.
"I am going to phase the engine through the train," Kitty replied.
"What? No, you can't do it. It's too much," Kurt warned her.
"There is no other choice, Jean can't stop the train in time," Kitty answered.
Jean pulls back as the engine nears the train. Kitty phases the engine, but about halfway through the strain is too much and she loses it. Kurt teleports them away as the engine solidifies and the two trains collide. A massive explosion occurs and Jean encloses it with a telekinesis bubble.
"I can't hold it," Jean shouted, when she was about to lose control of the fire. Lance arrives at the scene. He collapses the ground beneath the trains, burying them in the ground just in time. The fire is extinguished.
As the X-Men gather around Lance, he tells them, "It was my last of the heroic actions." And he walks away.
Later on in the news, the X-Men have been cleared of all charges, but the Brotherhood are now under investigation. Men show up at the Brotherhood house to take back all of their new stuff.
Everyone is pretty dejected. Pietro asks if they want to go into town on the new subway train and they all turn on him and start beating him.
—
In a cafe in Bayville, Ray, Bobby, and Jamie whine at Logan about having to take Scott and Jean's new class. They beg Logan to take over the class, but he refuses, "Scott and Jean have something to teach them, they'd better listen."
Logan leaves, then he picks up a scent and follows it into an alley. Tentacles break out of a wall and hit Logan with a neutralizer.
Logan wakes in a cell. He breaks free and slices a hole in the wall. It turns out he's actually in a transport plane.
Guards enter the room and blast him out of the plane, and he drops in a snowy forest then in the water.
From the other plane two people came out, they were Omega Red and Gauntlet.
Logan crawls out of the water where he came to rest and struggles onto land. He gets blasted again and knocked down a hill. Omega Red finds him and drags him out.
"I have been waiting for this for a long time, Weapon X," He said to him.
"You can't do anything to me," Logan said while struggling against him.
"Yurike saves you one time, but this time I am going to leave you broken and suffering," Omega mocked him and started torturing him.
Laura shows up and frees Logan and as she leads him away, Gauntlet reports to someone on the phone, "The target has arrived, the X-23 in play."
Laura gets Logan to a safe distance, and warns him, "You need to leave Logan. I left the Institute to protect you and the others from H.Y.D.R.A. Hydra and S.H.I.E.L.D. will continue to hunt me as long as I am alive."
She tries to get him to leave again, but he follows her, "The only reason you are here is as a setup to catch me, because they know I will save you."
Omega Red and Gauntlet continue to track Logan and Laura. While this is going on, Gauntlet continues, leaving Omega Red behind to catch up later.
Logan and Laura continue to move, aware that they are still being pursued.
"We are led into their trap, kid," Logan tries to tell Laura.
"You don't know what you are talking about," Laura dismissed him by saying.
"It's all experience, kid," Logan replied, but she again didn't listen to him. "You have to trust me kid, let me help you," He tried to stop her again.
"No one can help me, not you, not anyone. The only way I will get freed. The only way Hydra and Shield stopped hunting me, is if I am no longer alive," Laura said.
"Kid, you and I are into the same kind of thing. And even though they took my memories away. I proved it can get beyond this," Logan also explained his painful life.
"I wish they took my memories away," Laura said in a sad tone, then she turned towards Logan.
"If you want to help me, stop following me."
But soon they realize they're cornered. Gauntlet uses a sonic weapon to incapacitate them.
They're taken to H.Y.D.R.A. HQ, where Madame Hydra conveniently meets with Logan, "Welcome to Hydra, Weapon X."
"Where is the girl?" Logan asked her.
"Back where she should be, within Hydra the people who own her," Madame Hydra replied.
"Why can't you just leave her alone," Logan asked back.
"Leave her alone, she is the one who is hunting us," Madame Hydra laughed at Logan.
"Oh yeah, you are just the victim here," Logan taunts her.
"She has been on a crusade, to find and destroy everyone of our bases," Madame Hydra shouted in anger.
"Good girl, and you couldn't do anything about it," Logan praised the Laura while mocking Madame Hydra.
"We set traps for her, but she always manages to evade us, until now. Now we've recaptured her, we can finish what we started, we're going to wipe her rebellious mind clean and when we are done with her, X-23 will turn into the perfect weapon, which she designed to be, one without a emotion or free will," Madame Hydra revealed her plan.
"Madame Hydra, what about Logan," Omega Red asks her.
"He is no longer useful, like others, kill him," She orders and goes away.
"Logan, you know, you are the first of the Weapon X group including Sabretooth, Wade, and Maverick. But you will first have to pay," Omega Red taunts him, as he attacks Logan, but he misses and ends up freeing him instead. Logan knocked him out, and ran towards Laura.
Meanwhile the scientist working on Laura calls up Gauntlet to complain about him using one of the neutralizers on her, that it will interfere with the mind wipe.
As he finds out that Gauntlet didn't use a neutralizer on her, Laura's eyes open.
Alarms blair and soon Laura and Logan meet up in the hall.
"Come on, we are getting out of here," Logan tells her.
But she declined it by saying, "This is exactly the place I want to get it, the supreme Hydra is here. They did this to me." She shows her Adamantium claws.
"You wanted to get captured," Wolverine asked her.
"Yes, you should not be here," She revealed and started placing the explosives all over the base. But suddenly Omega Red comes and catches up with Logan and starts fighting with him.
Logan was able to knock out the Omega Red by putting his tentacle into an electric component.
Madame Hydra makes her way to the hovercraft to escape.
Laura climbs up the outside of the craft. Logan tries to follow and stop her, but she kicks him off.
On board, Laura confronts Madame Hydra. Hydra offers her anything she wants, but Laura replied back, "You can't give me what I want."
Gauntlet shows up to say that it's over and Laura agrees as she flings more explosives around the control room. She smiles wickedly at Madame Hydra just before the ship explodes and crashes to the ground.
S.H.I.E.L.D. shows up to arrest the remaining Hydra members, including Omega Red. Fury asks Logan about Laura, and he tells him that she didn't make it.
As they take off, Logan catches a scent and smiles. In the distance Laura watches them leave and then takes off into the forest.
Back at the institute Jean and Scott finally get the New Mutants to calm down and pay attention.
Wolverine walks by and smiles.