Spider-Man's progressing neogenic mutation is making him ill and he seeks the aid of a man known to help all mutants...Dr. Charles Xavier. In doing so he meets the X-Men but is disappointed to learn that Xavier does not 'cure' mutancy, only helps those born that way to accept and control their abilities. In the process of this endeavor though he becomes involved in a plot to destroy mutants everywhere. Will he be able to stop this hideous plan with the help of the X-Men?

Wolverine catches up with Spider-Man, hot on the trail of the missing Hank McCoy. Discovering his location and the plot to destroy all mutantkind the two team up and rescue Beast in the nick of time just as he was about to become the first test subject of Landon's horrendous plan. But when Landon accidentally falls victim to his own experiment he is changed into a giant monster that feeds on electrical energy. Can Spider-Man and the X-Men succeed in stopping this 50-foot tall, ohm-eating monster?

Worried that Kingpin is going to eliminate him after the botched framing of Peter Parker, Alistair Smythe arranges a meeting with Spider-Man to give him information about Kingpin. However, when Spidey arrives, he discovers Smythe has been turned into a cyborg. Part man, part machine, he is now the ultimate spider-slayer! However, when his programming malfunctions, he goes after the man he feels responsible for his father's death...Norman Osborn! Peter must fight a crazed Smythe, as well as his feelings when he discovers Mary Jane, the woman he loves, and Harry, his best friend, are engaged!

Ex-employee of Stark Industries, Dr. Jonathan Ohn, invents a portable interdimensional technology that accidentally makes him the living embodiment of a portal. Calling himself the Spot, he tries to steal money to fund his research. But his unstable invention has created a vortex that threatens to engulf New York. How can Spider-Man fight that?

When Dr. Ohn's Time Dilation Accelerator falls into the wrong hands all the criminal minds of the city vie for the portal technology. Peter and Mary Jane are celebrating Felicia Hardy's engagement to Jason Macendale when they overhear plans for a major heist!

Spider-Man captures a gang of thieves, and it looks like Robbie Robertson is their leader! Peter Parker and J. Jonah Jameson must team up to try to clear Robbie's name. But while Jameson returns to the skills he had as an Investigative Reporter, Peter must keep him safe from Tombstone. At the bottom of the whole plot is Richard Fisk, but can Spidey find the right clues to clear Robbie in time?

Doctor Octopus is blackmailing the mother of Felicia Hardy, and she begins to realize that her family has some dark secrets. Some snooping in the Daily Bugle files by Peter, and a confession by Anastasia Hardy, reveal that Felicia's father was really the Cat Burglar, a thief who got rich from the gains of an enormous heist. The Kingpin joins forces with Doc Ock to spring Hardy from jail, as Hardy holds the secret to the 1940s "Super Soldier" formula that created Captain America! To make sure the Cat Burglar cooperates, Kingpin kidnaps Felicia.

Felicia Hardy, now transformed into the Black Cat, is blackmailed into working for Kingpin, until he can replicate more of the "Super Soldier" serum.

Deborah Whitman has located Morbius, the Living Vampire, and brings him back to ESU to work on a cure. Just before leaving town, Felicia hears of this and uses the trip as an excuse to stay behind as the Black Cat. Together with Spidey and Whistler, she has to take on Herbert Landon and the Shocker in order to save Morbius from himself.

After a visit from an "old friend" of the family, Peter travels to Russia to investigate the mystery of his parents disappearance, and runs into some old friends!

Robbie and Peter encounter an old professor who knows about the Six Forgotten Warriors.

Spider-Man and the Warriors join forces to stop the Kingpin from activating the doomsday device.