At the end of the previous issue, Spider-Man was tossed off a bridge whilst chained up. After a few tries to shoot out a web line, he manages to shoot one which sticks to the bridge, but crashes into a support column as he does so, and is knocked unconscious. Whilst this is happening, the police have arrived around the column which the Jackal threw Spider-Man off of, and are threatening for him and Tarantula to come down. The Tarantula, the Gwen Stacy clone, and the Jackal all manage to escape, using a jet pack which the Jackal had hidden in her coat. The police also approach the unconscious Spider-Man, still hanging from his web line, but upon them untying his chains, Spider-Man reveals that he had been faking unconsciousness so that they wouldn't shoot him, them escapes.
Spider-Man then returns home as Peter Parker, where he finds Mary Jane. However, Peter has a lot on his mind with the return of Gwen Stacy, and pretty much ignores her. A moment after she leaves, he realizes what he's done, but can't do anything about it. A bit later, Ned Leeds comes to visit Peter, and tells Peter what he's worked out about Gwen Stacy. He says that the clone would have been created for revenge on either him or Spider-Man, since he loved Gwen, and Spider-Man was blamed for her death. He also adds that whoever cloned Gwen had access to her cell tissue when she was alive. Peter works out what's happened, and tells Ned that when Gwen was alive, they gave cell samples as part of an experiment to Professor Warren's assistant. Ned says that if they can work out what happened to the samples, they can work out who cloned Gwen.
Ned and Peter go to Empire State University, and ask Professor Warren about what happened to the cell samples. Upon checking the refrigerator where he kept them, Professor Warren finds them gone. Professor Warren says that his assistant, Anthony Serba, could have taken them, but has been missing for a while. Peter and Ned then split up, with Ned going to the Daily Bugle to see if anyone's found Gwen, and Peter trying to find Serba's address.
Peter changes to Spider-Man after finding the address, and enters Serba's apartment, but finds the Tarantula waiting there. Spider-Man is having difficulty in the darkened apartment, before managing to take the fight outside, where he quickly defeats Tarantula. However, moments afterwards, he is attacked from behind by the Jackal. As Spider-Man loses unconsciousness, the Jackal decides to reveal why he managed to sneak up on him. The Jackal says that Peter has always considered him a friend, then takes off his mask to reveal that he is Professor Warren.