Continuing from AMAZING SPIDER-MAN ANNUAL #13! Will Spider-Man finally defeat Doctor Octopus?
At the start of this annual, continuing on from the story in Amazing Spider-Man Annual #13, Spider-Man is clinging to a wall, noting how stormy the weather is after his encounter with Kent Blake. His spider-sense then starts tingling, and he wonders why it's tingling for a moment, when the wind suddenly starts to break down the wall he's on. Spider-Man manages to use his strength to stop the wall from falling down on the civilians, but the police demand that he can't just walk away from a near disaster without an explanation. Spider-Man ignores them and heads downtown to the construction site where he fought Doctor Octopus earlier (in the aforementioned Annual). Spider-Man finds Doctor Octopus's arm which he ripped off him, and thinks about how odd it was that Octopus screamed out when the arm was taken off him, almost as if it were a real part of him. He then heads for Empire State University to analyze the arm at the laboratories there.
Meanwhile, in his subway hideout, Doctor Octopus is being treated by a physician, who is telling him that there should be no physical pain, and that the pain of losing his arm is in Octopus's mind. Octopus gets angry at this, as he takes this as being told that he's mad, and so grabs the physician with his remaining arms and slams him into the ground. He then decides that it's time for his plan to go forwards, since he's recovered the documents which his henchman Ryan had stolen from him. Before he can do so, though, Octopus has to get his ripped off arm back.
The next day, at Empire State University, Peter Parker is heading into the physics building when his fellow student, Marcy Kane, arrives and tries to apologise for teasing Peter for running off when Swarm attacked the campus (in Spectacular Spider-Man #37). Peter doesn't accept her apology, and gets annoyed when she also starts disagreeing with Peter taking crime photos for the Daily Globe to make money. Peter then leaves Marcy, and goes to the laboratory to analyse Doctor Octopus's arm, which he brought with him in a bag. However, whilst checking it for a trace of radiation, the arm comes to life and attacks Peter. Guessing that Octopus is guiding it from afar mentally, Peter loads a web shooter and fires some webbing at the arm.
The webbing keeps the arm held for a moment, but it soon escapes and knocks Peter out of the window as it leaves. Peter manages to throw a spider-tracer at the arm before it escapes completely, then climbs back into the lab. Marcy then comes in and asks what all of the noise is about, and Peter flimsily says that his experiment got away from him. Shortly afterwards, Peter changes to Spider-Man and follows the arm, guided by his spider-tracer. He eventually follows it to a half-submerged oil tanker on the East River, and then finds the arm on the deck of the oil tanker. A moment later, though, he realises that the arm is just a decoy, and Doctor Octopus appears, with the missing arm reattached. Doctor Octopus and Spider-Man then have a lengthy battle, but despite everything Spider-Man tries, none of it seems to affect Doctor Octopus.
Spider-Man eventually runs below deck, but soon realises that he's outsmarted himself, as the cramped space gives Doctor Octopus an advantage. He also recalls that he's fought Octopus on a ship before, and that he was almost beaten that time. Octopus then shoots ink out of his tentacles, blinding Spider-Man and allowing him to get a few more hits in. Spider-Man tries to escape, but the walls of the oil rig are covered with oil, and so he slips back down into Doctor Octopus's arms. Octopus manages to knock out Spider-Man, then takes him back up to the deck. One of Octopus's henchmen offers to shoot Spider-Man and get rid of him once and for all, but Octopus decides that that would be too quick a death for Spider-Man and so throws him overboard into the water to drown. A spherical vehicle then arrives, which Octopus calls his Octosphere, and he and his men then get into it. The Octosphere then goes below the water, ready for Octopus's master plan to take over the world to commence.
Spider-Man suddenly re-emerges from the water nearby, having recovered consciousness. However, he's too tired and beaten up to swim for shore, so lets the current take him along the river until he is eventually taken out of the water by some members of the U.S. Coast Guard. They then demand to know what Spider-Man is doing in a restricted area, and when Spider-Man asks why the East River is suddenly restricted, they inform him that the Pentagon is testing an ultra secret atomic submarine in the area. Spider-Man then leaves, as he realises that Octopus's plan is to steal the submarine, as all of the clues fit together- Ryan stealing Octopus's plans, Kent Blake's appearance as a federal agent, and Doctor Octopus having an aquatic base.
Spider-Man then heads to where the atomic sub is, but the guards there think that he's there to steal it, and so fire at him. Spider-Man manages to avoid their shots until Octopus arrives, who easily brushes Spider-Man aside before jumping into the submarine with his men and taking it underwater. Spider-Man knows that he can't allow Octopus to get away with America's latest weapon, and so dives in the water after them. Spider-Man manages to open up the submarine hatch before the air in his lungs runs out, and the sub immediately begins taking on water. Spider-Man fights his way through Doc Ock's thugs until he reaches Octopus himself, and the two of them then fight. As their fight goes on, neither is able to gain an advantage, and Spider-Man eventually decides to get out of the sub before it sinks completely.
Spider-Man manages to escape to the surface, and just behind him is Octopus, who tries following Spider-Man to the surface. However, one of his tentacles gets caught in the hatchway, and Octopus is pulled down with the submarine, and appears to drown. With Octopus and the submarine gone, and no threat of danger from them, Spider-Man decides to head home before he catches pneumonia.