On TV, the X-Men hear about the events happening in Queens. Reporters are only allowed as far as the Queens-borough Bridge, and not even the traffic coptors can get a clear sight on what’s going on. But they are certain that super-powers are involved in the case. Kitty is shocked to hear about this and Wolverine asks her if she thinks her boyfriend is involved.
The reporter continues that the people living in the area have been evacuated and woken up by SHIELD agents from their sleep, and they have no idea what’s going on either. But, the reporter adds, numerous sightings of Spider-Man have been reported for months there. Plus, he reminds the viewers, there are rumors of Spider-Man either going or teaching at the high school not three blocks away. The reporter says that an anonymous person said to him: “What Nick Fury wants, Nick Fury gets.” He interviews Mary Jane’s mother, who cries and shows the viewer of her almost sixteen year-old daughter who’s still missing since this afternoon.
Kitty rushes to the Professor and phases through the walls of his office to get there faster. She interrupts a talk between Xavier and Scott and warns them about what’s going on with Peter, but Xavier thinks if Nick Fury is there he’s just doing his job, and believes that it could be Peter isn’t in trouble at all. However, Kitty believes differently, and shouts at Xavier to get the team into their uniforms, reminding him that Peter was there to help the X-Men out at every turn. Now it’s their turn to return the favor. Scott understands and smiles at the Professor that they’re going to Queens.
At a local hospital...
Sue Storm and Richard walk with the doctors and nurses into the hospital, with May on a stretcher, still suffering from her heart attack. The two introduce themselves to the doctors, who ask them both to wait there. Richard asks Sue if May is going to be all right, but she just responds to let the doctors do their jobs. Richard stares quietly in front of him, but Sue stares at him with a doubtful look. She asks a nurse if she can borrow some needles and a computer. The nurse says it’s okay, since Sue is from the Fantastic Four, and the fact she’s a Ph.D.
Sue sticks the needle into the finger of Richard, who wants to know what she’s doing. She just wants to test a theory. She looks at the sample through a microscope, and then types something in the computer. Richard still doesn’t understand what’s going on.
Peter is angry when he’s confronted with Dr. Octopus, and wants to kill him for destroying his house, cloning him and Gwen. However, he’s being held back by the female Spider-clone; Jessica. Octavius smiles that it’s good to see Peter again. Fury asks Octavius if these are the clones. Octavius confirms it, and informs Fury that the clone with the extra arms on the floor is also one of them. Fury orders all the Parker people to go stand against a wall.
The Torch asks Peter what’s going on. Fury warns Peter that he doesn’t want a big spider-fight coming out of this, and this situation is contained as of now. Reed asks Octavius if it’s true he created all these clones, which Otto confirms. He explains that, for the female clone, they denied a test clone its Y-chromosome sequence in phase two, which worked. Reed is shocked hearing that, and Fury asks everyone to take it easy. Jessica can’t believe Octavius made her. Octavius smiles he’s telling the truth, and was there when Jessica was born. She wants to kill him, but Fury won’t let that happen and points his gun at Jessica to hold her back. There has been enough killing tonight.
Octavius wants to keep it civil as well. It’s been a long day and he missed dinner because of this. Johnny and the Thing walk over to Peter and ask him what happened to Mary Jane. Peter explains to them she’s been infected with Oz, which is a chemical, and now these clones ruined her. A clone with a partially scarred face – the one who did this to MJ – claims MJ’s all right. As Peter cries and tells him to stop, Johnny powers down and admits to Reed he’s freaked out by this. He knows MJ and asks Reed if he can fix her. Fury denies that, which Johnny doesn’t understand. Fury adds they’ve got a situation there that needs to be contained before the “Fantastic Four” do something out of control.
Johnny angrily flames his fists on and points them at Fury, threatening him that Reed’s going to take MJ to the Baxter Building and fix her. She’s just a civilian and he doesn’t think Fury’s going to get in their way. Fury shouts that, if Johnny isn’t going to help this situation by obeying orders, he wants him out of there. Peter holds MJ in his arms, and begs everyone to help her. The Thing takes her over and Reed promises he’ll do everything he can to help her. Fury dislikes this.
The clone with the scarred face panics when MJ is taken away from him. Jessica does her best to hold him back, but fails and the clone jumps into the attack. The SHIELD agents open fire on the clone and hit him. Jessica fights the agents and Fury shouts at everyone to stop this at once! Everyone calms down and the agents point their guns at Jessica, who puts her hands in the air. Fury orders the Fantastic Four out of there, and they leave. Reed glares angrily at Octavius, who tells Reed not to give him that look. He knows how he and his family got their powers. He doesn’t see any difference here, other than the fact he did it all on purpose. The Thing tries to call Octavius names, but Reed calms him down and says they need to get out of there.
Octavius grins that he appreciates Fury’s good work in such a tense day. And these sentry drones are quite impressive to him. But, he adds, this is their problem and says they’ll have transport ready to take all these young subjects back to safekeeping. Fury refuses and reminds Octavius that he has a lot to answer for. Octavis knows that, but he doesn’t have to answer to Fury. Fury defends Octavius has, because this little house of horror he created has now dropped onto civilians, which means he’s under arrest. Otto remains calm, suggesting that Fury first calls his supervisor before he does anything like that. Otto wonders who that was. Does he wonder why he didn’t know this project was happening? Even though he’s the big super hero big shot of the world? Peter wants to know how Octavius did this and why he’s not in jail. He has to tell him! Fury again reminds Peter to stay calm.
Octavius doesn’t know what he has to tell Peter. Should he tell him that he was going to prison after he beat him up on television, but that instead he made a deal with the federal government to work for them... to help them design a super soldier? It seems there are a great many people in the United States that truly hate Nick Fury and his little band of self-loathing super heroes. And they don’t want Nicholas Fury to be the only person in the country with his finger on what they call “the Captain America” button. Both Peter and Fury are shocked to hear this.
The doctors continue to operate on May. Sue continues her research and the computer reveals there’s a 99.342% match sample of Peter Parker to be found in Richard’s sample!
Octavius explains to the clones that because of his “relationship” with them that he was able to take the blood sample and understand the unique qualities. And from there he was able to clone a female version of Peter. He was able to mutate and biograft him. He was able to tamper with one of the clones’ aging process and even convince it, through psychic memory implants, that it was Peter’s father. “What?” a shocked Peter wonders.
Sue stares at Richard, who can’t believe what she just discovered. He walks away quietly.
Octavius further says that, thanks to the good people at the Federal Bureau of Investigation Special Projects Research and Development... he got to continue his work. Which before he became “Doctor Octopus” and before there was a Spider-Man or a Norman Osborn... before all this nonsense came down on his life, that’s who he was: his work. Fury tells Octopus he’s under arrest. Fury tells Octavius he’s under arrest. Otto smiles he isn’t as he has credentials. And he has rights. And, he is not in Fury’s jurisdiction.
Peter and Jessica both still wonder how Octavius made them. He reveals that they had a blood sample of Peter Parker. They confiscated that from Peter’s friend, Doctor Curt Connors. Well actually, Connors’ assistant, Ben Reilly. Otto calls Ben a good man. And with it they went to work. And they’re in phase three of a super-soldier experiment. And Jessica is the proof that it’s working.
Peter angrily glares at Otto, wanting to attack him, but Fury holds him back. Otto mocks Peter, thinking little Spider-Man is going to cry. He reminds Peter that he didn’t do anything to him. This isn’t about Peter. This is about Otto’s work. He claims it just so happens that his work completely perverts and destroys every single part of Peter and his life! Otto calls this the most important scientific breakthrough since Bruce Banner discovered radiation mutation. This is it, and Otto is glad he did it. It wasn’t Peter’s daddy, nor Reed Richards, not Norman Osborn or Tony Stark. It was him. And next year, Octavius grins, when a thousand Thors descend on the Middle East and put that situation to rest once and for all, he will be given the Nobel Prize and a medal of honor. Otto promises he’ll thank Peter for it. Peter is shocked to discover that his father... isn’t really his father!
Richard looks at May, who’s still being operated on. Sue suggests they go for a walk but he doesn’t want to leave her. Sue tells Richard they’re doing everything they can for May and they shouldn’t be there. When Richard asks what’s going on, Sue takes his hand, and they go for a walk.
Octavius explains to Peter that his father died in a plane crash. He thinks Peter really deluded himself if he thought that man he saw earlier was his father. Otto smiles and jokes that he thought Peter was supposed to be smart. Fury is stunned. Peter looks ashamed. In tears, he angrily looks up at Octavius, who tells Peter he can look at him that way all he wants. He’s not the bad guy here. There’s lots of guns in this room... and they’re all pointed at Peter.
Peter suggests making a deal with Fury. He wants Fury to send his men for some coffee. He wants him and his clones to have ten minutes with Octavius. After that, he promises he’ll go with Fury and surrender. They’ll all do that. Octavius smiles that that’s cute, but reminds Peter that Fury isn’t in charge of this situation. He asks Fury to do something useful and round up all the Parkers there. He mentions that the fed team is on its way for cleanup. Fury can use whatever force necessary. Fury doesn’t know what to think of that but Otto remarks that he can always make more. Fury smiles to his troops that they heard what Octavius said. He orders everyone out and wants a perimeter set around the building. He orders Tinkerer to slide the slayers out.
Octavius, a bit surprised, asks Fury what he’s doing. Fury explains to Otto that he’s right: he isn’t in charge of this situation. Otto is. And Fury wants Otto to go be in charge. Peter and Jessica are glad to hear that, but Otto freaks out and orders Fury to come back and do his job. However, Fury and his men just walk outside, reminding Octavius about where they’ll be. He closes the door.
Peter and the other clones angrily glare at Octavius. He doesn’t want to engage himself into any of this, as this is not the life he wants for the new him. The clones all start fighting Octavius, and the clone with the extra arms asks who wants first dibs. Octavius asks Peter if hitting him is going to make him feel better. Peter jumps at Octavius wanting to strike him, but Octavius then throws bricks into his face! Octavius claims that he wasn’t going to bring it to this level! The clone with the extra arms holds Octavius by his clothes, with Otto saying that he worked so hard to keep this part of his life secret. The arm-clone gets punched away, and Jessica is shocked at what she sees.
Otto panics and shouts out: “My arms. My metal arms! The ones that made you think it was so funny to call me Doctor Octopus!” Octavius’ arms come out of his back, and they kill the clone with the extra arms. Otto claims that it wasn’t his arms: it was the metal. He could control the metal! Peter and Jessica both once more look in shock at the new metal arms that come out of the back of Octavius, who is now ready for battle.