-The Kingpin looks over his balcony at the city below him... He smiles, turning to face the psychologist Aunt May was seeing a few arcs ago. He asks her if she's absolutely sure. She says that she came directly from her office where the boy's aunt had told her. She says she knows about the Spider-Man problem because she dated one of his crime bosses briefly a year or so back. Kingpin thanks her and asks one of his men to walk her out and to make sure she gets the money she was asking for. She starts talking while she's walking, saying how she needed the money to keep her business running, and how nervous she was, they reach the elevator and the door opens, and the man pushes her down the empty corridor. There is a small thud as she hits the ground two stories below.
He calls out Mr. Larks, who steps out of the shadows. "Confirm This"
-The rest of the story would be Peter being at school, unable to concentrate because of all the **** he'd been through in the past few weeks... The Bell rings for lunch and he puts on the costume, and leaps off the roof to swing through the city a bit. Mr. Larks steps out of the shadows, camera in hand, and cell phone up, he says, "confirmed." Cut to Kingpin, who is grinning wildly... "Then lets end this, once and for all"
- Peter goes to school the next day only to be called to the principal's office. The principal asks him if he's seen flash gordon lately, and Peter says he hasn't. Flash was apparently beaten close to death, and he has said that it was Peter Parker who did it. Peter says he didn't, but the principal says that he's seen pictures, and that Peter shouldn't lie to him, because the authorities are going to be here to pick him up shortly.
- The Kingpin watches the events unfold through a camera placed in the corner of the office. A man behind him walks out of the shadows. He is wearing a white mask over his face. Kingpin tells the man that his Chameleon Mask seems to have done the trick, and that he can take his money. He says that he suspects they'll meet again.
-In a police car Peter starts to think through who would try to frame him for this, and who would give out that information. And who could be hurt for this information getting out in the first place. He breaks out of the police car, kicking through the door, and runs to his old house, and breaks in. Aunt May is there and asks him what the hell he wants.
- Peter asks if she told anyone that he's Spider-Man and she says that she told her psychiatrist. Peter tells her that he's been expelled and framed for the brutal beating of one of his fellow students, and that the police will be waiting at the apartment he has been living in since he was emancipated. "They'll be here too, soon" she says. She told them that peter would come, and to send some squad cars. Peter asks her why she's doing this, and she says that Peter betrayed her trust and she never wanted to see him again. He says that he could go to jail, and she says "good." "get out of my house before the police get here, or i'll turn you over myself." He pauses, and runs up the stairs. Pausing at the top to tell Aunt may that he loves her, and that he's sorry he had to put her through all of this. She hears movement on the roof as the cops get there. She is crying.
- Mary Jane and her parents are at the hospital she has been staying at since the events of the Clone Saga. They are watching the news, where it is announced that award winning student Peter Parker has escaped from Police Custody after being charged with the assault of Flash Gordon.
-A Nurse walks into MJ's room and asks her Parents to come with her for a moment, saying that its urgent. Mr. Watson starts asking whether Parker has anything to do with it, and she says to come now. In the next room the nurse pulls out a gun, and shoots the parents in the head. She goes out back out into the hall where you can see that the entire hospital staff has been killed. She walks back into MJ's room, only to see that the bed is empty and the window is open. She calls the kingpin and says that the girl has been taken. He says very well, and then tells her, "When the police get there, You are a disgruntled nurse who is taking out her frustration on her patients. If you implicate me your daughter will be killed, if not than we will pay for her transplant. It has been a pleasure doing business with you, ma'am."
-On the roof, Peter tells MJ that he saw the woman kill her parents, and that its probably the same person who is framing him for Flash Thompson's assault. MJ lashes out at him, because it is his fault that she's in this mess, and that its his fault that her parents are dead. And he yells back that this is why he tried to push her out of his life. She starts crying, and he holds her, and starts crying with her, realizing that his life has just changed again for the worse.
-(A Few Days Later): MJ walks into the headquarters of the CIA in Washington DC. She says she needs to talk to Richard Parker.
- Stealing the materials, Peter finishes a makeshift costume, red, with a blue sweater with a spider on it (*cough* scarlet spider), he also retrieves his back-up web-shooters from his gym locker. And visits his High School principal to ask him who showed him the pictures, then he goes and visits a police officer at home and then winds up finding an employee of Richard Fisk... In his anger he beats him up really badly as he realizes the Kingpin set him up, which is caught on tape. The man had no idea what he was delivering, he was just happy to be asked to do something by the head of his company. He viewed it as him being in line for a promotion.
- The tape finds its way to the Daily Bugle, where Ben Urich is told that he has to write the story of Spider-Man beating the **** out of an innocent man. He watches the tape and sees that Spider-Man is getting out of control, and writes the story.
- Peter sees the Daily bugle and he tears it apart, unable to deal with his life slowly falling apart
-In DC, Richard Parker meets with MJ, and she tells him that Peter is being set up by the Kingpin. He says that he knows, but there's nothing he can do... People are afraid of getting themselves killed... They can't move on Kingpin unless he makes a documentable mistake. He offers MJ to stay with him for the time being. She accepts.
- Peter fights the Kingpin, and loses badly, breaking his arm as he is thrown from the building.
-He manages to get to Hell's Kitchen, collapsing while screaming out for Daredevil in the rain. He wakes up on Matt Murdock's couch. Peter asks him where he is, and where his costume is. Matt tells him that he's safe for now, but that he clearly doesn't know what he's doing, and that he shouldn't be doing this, as he's clearly in over his head. Peter tells Matt that his life has been taken from him, and he's in too far just to give it up.
In the following six issues:
- Peter lives with Matt Murdock, takes up the identity of Ben Reily (from his uncle's name, and his Mother's maiden name), dyes his hair blonde, and starts working as an intern at Nelson & Murdock.
- Daredevil trains him to fight, and Spider-Man sometimes joins him and the Ultimate Knights as they fight crime in the city
- They hunt down the chameleon, and force him to testify against the Kingpin and to clear Peter's name.
- The Knights break into The Kingpin's office and tell him that one of these days he's going to fall, and he's not going to get back up. The Kingpin smiles and says he'll leave them alone for the time being, because they aren't worth his effort. Once they leave, he hints at his next scheme to bring back his wife, and he tells her he's sorry he let himself get wrapped up in another bout of revenge like the one that left her in her coma.
- Peter goes to DC to get Mary Jane, and she gets angry with him for having taken her life away and then shipped her off to not deal with for months as he fixed this. She says that she'll stay in DC for the time being, and that she doesn't want to see him for the near future... She needs to figure out a few things in her life, and she can't do that with Peter around.
- Peter keeps his job at Nelson & Murdock, and Matt tells Peter that he can stay with him. Peter returns to school and he and Flash Thompson have a chat where Peter tells him that he's sorry that Flash had to get involved. Flash tells him that he's figured out that he's Spider-Man, and that he understands, and that he won't tell anybody.