Peter takes a new job as a Horizon Labs researcher, while Phil Urich becomes the new Hobgoblin after killing "Roderick" Kingsley and steals a sample of Reverbium (an experimental synthetic Vibranium substitute) from Horizon Labs for the Kingpin. With Hobgoblin's sonic laugh being a major obstacle, Peter uses his Horizon Labs equipment to create a new suit in order to counter Hobgoblin, and teams-up with Black Cat to retrieve the Reverbium.
Alistair Smythe jail breaks Mac Gargan to endow him a new Scorpion suit, created as part of a new army of Spider-Slayers with cybernetic implants. Their membership includes those with a grudge against J. Jonah Jameson, and Smythe equips his Slayers with a Spider-sense facsimile that makes them more difficult to subdue. As Smythe targets Jonah's loved ones to make him feel the pain Smythe felt losing his father, The New Avengers help Spider-Man against the Slayers. But with the losses growing and the heroes nearing defeat, Peter builds a bomb that will only destroy the "spider-sense" in the Spider-Slayers. But with Scorpion's prevention of Spider-Man from escaping the blast radius once the bomb detonates, Peter loses his spider-sense too and is too stunned to stop the remaining Smythe. As he attempts to kill Jonah, Marla intercepts to save him, as Spider-Man apprehends the villain. Holding his wife, Jonah blames himself and not Spider-Man.
With Smythe once again incarcerated, a funeral is held for Marla Jameson, and Peter's guilt over her death builds into a nightmare where everyone who has ever died in his life eat away at his conscience until Peter awakens, vowing to be a better Spider-Man. Facing off against Massacre, a new villain with no emotion and with a purpose of killing, Spider-Man is shot and injured in a fight. Peter then builds a new bulletproof Spider-Armor to combat Massacre, defeating the villain and saving numerous hostages. He confronts Jameson about his new stance, who wants to give the death penalty to Smythe for killing Marla and also to Massacre for all the innocent people he killed.
- As later revealed in Amazing Spider-Man #691, although the Hobgoblin that Phil Urich murders is presented as Roderick Kinglsey, it's Daniel Kinglsey, Roderick's twin brother pretending to be him.