Young Peter Parker must pick up the pieces of his life and face a series of terrifying questions: Will Aunt May survive her heart attack? What plans does Nick Fury have for Gwen Stacy? Is Peter being drawn back to MJ, or will he stay with Kitty Pryde? What about the mysterious Spider Woman? The answers will shock you.
Knowing that Mary Jane has recovered from being cured of the Oz formula, Peter goes to the hospital to see how Aunt May is doing after her heart attack. Nick Fury, Captain America, and Iron Man arrive at the Baxter Building shortly after searching for Peter. The Thing begins to argue with Fury about leaving Peter alone when Mary Jane reveals that Peter looked up to Fury. She said that Peter told her he wanted to be like him and wants to be the greatest hero in the world. All this is shocking to Fury.
Kitty Pryde and the X-Men arrive at Peter's house in Queens in the blackbird in cloak mode. They soon discover that Aunt May suffered a heart attack and head towards the hospital.
Peter talks with Sue Storm, who tells him that the man he thought was his father was, in fact, a clone of him. Peter said that he had figured that out. Left alone with Aunt May, Fury arrives. Fury informs Peter that the reason he had created the Spider Slayers prior to these events was because he was planning ahead. He figured that anyone that had gone through all the ordeals that Peter has, would turn into a supervillain. He then admits that he was wrong, much to Peter's pleasure. As Fury is about to head back to the Baxter Building, Peter asks Fury to tell Reed Richards that he's going to pass on his offer.
Kitty Pryde arrives at the hospital and asks Professor X to erase Aunt May's knowledge that Peter is Spider-Man. He refuses and she tells him that she hates him. It turns out that Aunt May is able to forgive Peter for his deception.
Peter finds Spider-Woman to see what she has planned. Even though things are good between Fury and Peter, she decides that she wants to be on her own. She leaves saying she thinks she'll give the super hero thing a try.
Peter returns home, or to the destruction that is his home. Mary Jane's mother tells Peter that he can stay with them. As Peter and Mary Jane embrace after everything that has happened, Kitty is shocked and saddened to witness this.
As Mary Jane wakes up to brush her teeth, her hand begins to shake. She then thinks she sees Peter's scared clone that had kidnapped her as Peter comes to check on her.