The story takes place right after Venomous.
Peter is confronted by Mac Gargan aka the Scorpion who tells Peter that Norman Osborn is the mastermind behind the whole scenario and told him Spider-Man's secret identity about a years ago. The Scorpion continues to tell Peter about the history of super-villaines, as they were formed in the 1950's by ruling class big buisness individuals who were afraid that super-heroes would discover their hidden agendas and questionable methods. They invested heavily in super-villains and even contracted them to fight specific heroes. Norman Osborn was one of their favorites who build his fortune thanks to their fundings until his Goblin personae became unstable and now that he's in jail, he has become a liability since he can expose the doings of many high profile individuals. So now, Osborn is vulnerable in jail and Doctor Octopus has been brainwashed to kill him this weekend. Norman has orchestrated the kidnapping of Aunt May in order to solicit Peter's help in breaking him out of prison and if he doesn't May dies.
Though reluctant, Spider-Man teams-up with the Black Cat and successfully break Osborn out of jail. However, Norman, dressed as the Green Goblin, double crosses them and introduces to the newly formed Sinister Twelve which consists of himself, Chameleon, Shocker, Lizard, Rhino, Hydro-Man, Sandman, Vulture, Electro, Boomerang, Tombstone, Hammerhead and Scorpion who has become the new Venom after he bonded with the symbiote after it left Angelo Fortunato to look for a new host. The Green Goblin then orders the twelve to attack Spidey and the Cat while he goes to murderer Mary Jane, pleased that Spider-Man's last act was a criminal one. Spidey and Felicia desperately try to fight back against the villaines but they are overwhelmed by their sheer numbers and Cat is struck down by Electro, much to Vulture's displeasure because he wanted to get her first for what she did to him. Before the final blow was about to be struck, Captain America, Daredevil, Iron Man and the Fantastic Four appear thanks to Mary Jane having called S.H.I.E.L.D and they neutralize the villaines. Peter goes to rescue Mary Jane from the Goblin but he is ambushed by Venom who continuously taunts Spider-Man about what they're going to do to MJ. Angered, Spidey defeats Venom by dropping a building down on top of him using his webbing.
Spider-Man then comes across the Green Goblin holding Mary Jane the same way he held Gwen Stacy years ago on top of the George Washington Bridge. The Goblin tells Peter that May is still alive but that could change in the next 45 minutes and tells him that he's not "Down Among the dead men" yet. As Norman is taunting Peter, a brainwashed Doctor Octopus appears and distracts him, giving
Peter the chance attack and bring Mary Jane to safety. As they fight, MJ pulls out the gun she's been carrying and shoots the Goblin in the chest but the impact causes her to fall off the bridge, only to be saved by Spider-Man who uses multiple strands of webbing to minimize the impact so that she wouldn't die like Gwen. The Goblin attempts to impale Spidey with his Glider but he is attacked by Doctor Octopus again and they are both struck down by a lightening bolt and end up crashing down into the waters below.
Peter and MJ embrace and he finally figures out where Aunt May is. Following Norman's clue about being "Down Among the Dead Men", Peter goes to Uncle Ben's grave and finds his aunt buried alive in Ben's grave site, sustained by oxygen.
Ock was found by the Avengers and the police and Norman has disappeared. Gargan has been arrested and wants to be called Venom from now on and his old Scorpion suit has been auctioned off. Peter visits Black Cat in the hospital and he realizes that she still has feelings for him. Thinking that Spider-Man is his own son John, J. Jonah Jameson is now using his paper to support Spider-Man.
In the conclusion, May tells Peter that she's proud of him and he receives a letter written to him by Norman, thanking him for providing the intellectual and physical challenge as Spider-Man as they have provided his life with both structure and meaning.