Story
It is two years following the events of the first game. Spider-Man is trying to balance his civilian and superhero life, frequently late or absent for school, work, and leisure time with his friends. Following dinner with Mary Jane Watson and Harry Osborn, Peter thwarts an armed looting of a museum, and tracks down an escaped robber, the Black Cat. Soon after this, he thwarts an attack in the streets of Manhattan by The Rhino. Meanwhile, Doctor Otto Octavious attempts to recreate Nuclear fusion of that seen in the sun to provide an energy source for Manhattan. To control this fusion, he creates four metal arms which he can mentally control. His fusion creates a strong magnetic field, destroying the lab, killing his wife Rose, and grafting his metal arms to his spine and giving his arms control over him. He blames Spider-Man for the incident.
Octavius, now known as Dr. Octopus, kidnaps Aunt May, but she is saved by Spider-Man. In the time following, special effects artist Quentin Beck tries to prove that Spider-Man is a fraud by challenging Peter in a series of "games". Spider-Man emerges successful. Consequently, Beck tries to kill Spider-Man, but is thwarted. The embarrassment causes Beck to assume the identity of Mysterio, attacking journalists attending his press conference, and commands his "UFOs" to "invade" the Statue of Liberty. Both of these attacks are thwarted by Spider-Man's efforts, with no casualties. Spider-Man eventually teams up with Black Cat, who leads him to the Shocker, who escaped during Beck's initial competition with Spider-Man. Shocker is apprehended in a warehouse after attempting to use an experimental propulsion system to enhance his powers, while Mysterio is knocked out with one punch from Spider-Man while trying to rob a Speedy Mart. Black Cat then leads Spider-Man to an illegal weapons trade, where she tries to convince him to permanently become Spider-Man, but he rejects the idea, saying that he cannot stop being either Spider-Man or who he is.
Dr. Octopus kidnaps Mary Jane Watson and steals Tritium from Harry Osborn to repower his nuclear fusion in exchange for Spider-Man. A long battle on top of a bridge leads to Peter being delivered to Harry. Peter reveals his identity to Harry, and sets off to defeat Dr. Octopus a final time. The fusion reactor is shut down, and Dr. Octopus regains control over his mind and his sanity back, and sacrifices his life to permanently destroy his fusion reactor.
The next day, Peter gets a surprise visit from Mary Jane, who tells Peter that she cannot live without him, and wants to offer her full support to his life as Spider-Man. With his confidence renewed, Spider-Man continues to defend the city from evil.