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When the burglar breaks in, he kills Aunt May instead of Uncle Ben. Peter goes after the burglar and ends up killing him. Before the police arrive, Ben gets there and has Peter leave, confessing to the cops that he was the killer instead. He's sent to prison and Peter ends up giving up being Spider-Man as a hero.
Later Peter is put into a Juvenile Detention Center for breaking and entering and assault against J. Jonah Jameson, who was broken up over his son, John Jameson's, death on the shuttle.
In Juvie, Peter meets Harry Osborn and Flash Thompson, who are there for different reasons, but overall don't care for Peter. He eventually escapes, and goes to work hunting super villains for bounty money. He is sent after the Green Goblin, who had killed some innocent people, and ends up putting the Goblin in a coma.
Peter eventually attempts to use his abilities to break Ben out of jail, but Ben refuses to leave, instead giving a speech that turns Peter's life around.
When Ben is released, he helps Peter become the man they both always wanted him to be.