At the start of this annual, a mysterious man arrives at an office building, thinking to himself that he has to contact "home base" before it's too late. However, inside the building is another man who manages to push the first man out the window, not wanting the man to say what he knows. As the man dies, his murderer wonders whether he was too late, and that the man got a message through to the government.
In an abandoned subway tunnel, Doctor Octopus rages, as his plans for some scheme have been stolen. At first he accuses the members of his gang as having taken them, but one of them accuses the gang member Jimbo of having taken them. Octopus decides that Jimbo will pay for stealing from him.
Meanwhile, Spider-Man finds some criminals breaking into a warehouse, apparently lead by the same Jimbo from Doctor Octopus's gang. Spider-Man manages to defeat the thugs, but Jimbo manages to get away in the confusion, with Spider-Man not knowing yet that Octopus is out to get him. After the police have arrived and gotten rid of the gang, Spider-Man starts to wonder where their leader went. A mysterious man then appears without Spider-Man noticing, and tells Spidey that the man Spider-Man is looking for killed a Secret Service agent named Kent Blake. Unfortunately, the agency Blake worked for thinks that his death was suicide, and this man knows that it wasn't. He wants Spider-Man's help to prove that Blake's death wasn't suicide. Although Spider-Man is hesitant, the man convinces Spider-Man to go to Blake's funeral, and make up his mind then.
After going to the funeral as Peter Parker and meeting Blake's widow, Peter goes home to think about what to do. The mysterious man then appears in Peter's apartment, and asks Peter if he'll help. Peter feigns surprise at this, but the man pulls aside Peter's jacket to reveal Peter's Spider-Man costume underneath. Peter then confirms that he'll help, and the mysterious man gives Peter an address to go to. Peter then goes there, which is apparently Jimbo's headquarters. Disguised with a rough beard and some sunglasses, Peter asks to join the gang. At first Jimbo is refuses due to Peter's age, but after subtly demonstrating his super strength, Jimbo agrees to let Peter join his gang.
Later that night, Peter and the rest of Jimbo's gang head to a ship, which is where the parts for a super weapon described in the plans that Jimbo stole from Doctor Octopus are being kept. The gang sneaks onto the ship, but are seen by a guard. Jimbo pulls out a gun, ready to shoot the guard, but Peter can't let him shoot the man without giving himself away. He then subtly uses his web shooters to pull the man away just as Jimbo shoots, making it look as though the man was shot, when in reality he was just pulled to the ground and knocked unconscious from the fall. Jimbo then announces that the gang is going to get away with this, but Peter thinks that he's going to put Jimbo away for a long time shortly from now.
Doctor Octopus meanwhile breaks into a police station to talk to the members of Jimbo's gang that were captured by Spider-Man the previous night, and to find out their whereabouts. Unfortunately, they've been bailed out, and Octopus is found by the police. He manages to escape, and then goes on a rampage through the city, looking for thugs to question about Jimbo's location. Eventually, someone tells him where to find Jimbo, and Octopus breaks into Jimbo's headquarters, where Peter Parker is currently residing with the rest of Jimbo's gang. Doctor Octopus recognises Peter from a few previous encounters they've had, and blows Peter's cover in the process. He then manages to find out where Jimbo himself is, and leaves. The remaining thugs then grab Peter, since they know he's not a criminal like them, and throw him into the river to die.
Peter manages to get out of the river without drowning, and meets up with the mysterious man who wants him to prove that Blake's death wasn't suicide. The man gives Peter Doctor Octopus's location as Peter changes to his Spider-Man costume, but reminds Peter that he wants to take out Jimbo. Spider-Man then heads to Jimbo's apartment, where he finds Octopus attacking Jimbo. Octopus manages to get rid of Spider-Man temporarily, and when Spider-Man returns to the apartment, he finds both Octopus and Jimbo gone. The mysterious man is there though, and he tells Spider-Man to head for the Graham Construction site. A moment later, he disappears, and Spider-Man promises to question him once this is all over.
Octopus and Jimbo arrive at the construction site, and Jimbo admits that the plans he stole from Octopus are in a building across the road. Octopus then uses his tentacles to get them, before he's attacked by Spider-Man, who has just arrived. The two of them then fight more brutally then before, and at one point Spider-Man grabs Octopus by a tentacle and starts swinging him around. The speed causes the tentacle to rip off, causing Octopus as much pain as if one of his real arms had been ripped off. Whilst this is happening, Jimbo tries escaping, but is found by the mysterious man who has been assisting Spider-Man. Upon seeing him, Jimbo panics, and falls off the construction site in his attempt to get away from the man. Spider-Man swings down and saves him, but whilst doing this Doctor Octopus makes his escape with the plans which Jimbo stole. Jimbo is then arrested.
Peter later visits Blake's widow, whom he met at Blake's funeral. She shows him a picture of Blake, who looks exactly the same as the mysterious man who was assisting Spider-Man, implying that the mysterious man was Blake's ghost.