At the start of this issue, Spider-Man crashes through a window, since his spider sense has just started tingling. As Spider-Man looks around, he notices that for a seemingly simple apartment, it has a lot of high-tech equipment. He is suddenly attacked by someone who is hiding in the shadows, who tells him to keep out of his businesses. The mysterious person then runs off, and makes his getaway. As he tries to follow, Spider-Man is attacked by SHIELD agents, and he realises that the "apartment" is actually a secret SHIELD installation. Spider-Man manages to get away from the agents, but the mysterious person escapes.
At Curt Connors's house, Curt collapses as his wife and son enter the room. They ask him what's wrong, and he tells them that it's the after-effects of an explosion from a few days ago when he was trying to help Spider-Man (in the previous issue). The door is then kicked open, and Stegron walks in, and grabs Curt's son. He tells Curt that he has left instructions for Curt in his laboratory, and that Curt has 48 hours to follow the instructions, otherwise he'll kill Curt's son. Curt figures he has no other choice, and heads to his laboratory to work.
Peter Parker bumps into Flash Thompson, and tells him to stay away from Mary Jane, since he and her are together. Flash then explains, completely baffled, as he Mary Jane had suggested the two of them go out, and he had thought that she was single. He then says that he never would have tried anything if he had known that, and apologises to Peter. Peter accepts Flash's apology, but thinks to himself what an idiot he is for distrusting Flash. Whilst this is happening, J. Jonah Jameson and Marla Madison (whom Jameson met with a few issues ago) do some tests with a cybernetic helmet, and then start planning the defeat of Spider-Man.
Returning to Peter Parker, Peter has just met up with Mary Jane, and the two of them talk about how things are between them. Mary Jane says that she doesn't really know where they stand at the moment, since she had originally just been there as a friend for Peter after Gwen Stacy died, but they became more after they kissed when Peter left for Paris. She basically then says that she's not sure if she can handle a serious relationship, but sees the same thing happening to all their friends. As the two head to a light show, they decide that they'll see how things go between the two of them. As the light show goes on, the lights suddenly go out without reason.
At the Museum of Natural History, Stegron is using a special gun to reanimate some dinosaur skeletons, so that he can use them to take over humanity. As he continues, Peter Parker leaves the laser show to find out what caused the blackout, since his spider sense is tingling and telling him that it's not good, and runs into some of the dinosaur skeletons moments after changing to Spider-Man, which have come to life. After escaping from them, Spider-Man runs into Stegron, and the two of them fight, before Stegron brings down a wall on Spider-Man. Spider-Man manages to survive the wall, but after pulling himself out from the rubble, finds Stegron and the skeletons he's brought to life missing. Elsewhere, the stress of Stegron's threat combined with the explosion he took are having an effect on Curt Connors, as he turns into the Lizard, and announces that he's going to destroy Stegron!