Peter Parker has finally managed to strike a balance between his devotion to M.J. and his duties as a superhero. But this stability is short-lived when his Spider-Man suit mysteriously turns black, enhancing his powers but also amplifying the darker qualities of his personality that he struggles to control. As the suit's influence grows, Peter becomes arrogant and neglects those he cares about most. Meanwhile, the city heralds Spider-Man as a hero, leaving Peter basking in uncharacteristic public adulation.

Outside of Peter's personal challenges, new foes emerge to threaten New York. Flint Marko, an escaped convict, becomes engulfed in a freak accident that transforms him into the shape-shifting Sandman. Marko's desperate attempt to save his critically ill daughter leads him on a collision course with Peter's alter-ego. Additionally, Peter must contend with Harry Osborn, who continues to seek vengeance against Spider-Man, believing him responsible for his father's death. Harry adopts the mantle of the new Goblin, utilizing his father's technology to challenge Peter both personally and as Spider-Man. As Peter fights these battles, another adversary, Eddie Brock, a rival photographer, jockeys for position at the Daily Bugle and becomes entangled in the web of conflict. The arrival of an alien organism sets the stage for the emergence of an even greater threat that challenges the foundation of Peter's world.