he game opens as Peter Parker and Gwen Stacy sneak into the restricted areas of Oscorp after hours, where Gwen reveals her suspicions that they may be continuing Curt Connors' cross-species experiments. In the process, they are caught by Alistair Smythe, the new director, who explains that some scientists were indeed secretly continuing Connors' cross-species experiments by injecting animals with human DNA; said cross-species carry a powerful virus and are currently being shipped to the bio-lab for disposal. At that moment, the cross-species all react to Peter's presence and escape, infecting all of the scientists, including Smythe and Gwen, in the process. Peter quickly dons his Spider-Man suit and gets the infected to quarantine, fighting off Smythe's security robots in the process, but is unable to stop the cross-species from escaping into the city.
After fighting off one of Smythe's S-Bots, Spider-Man goes to the Beloit Psychiatric Hospital, where Dr. Connors has been incarcerated since the Lizard's rampage, and informs him of the incident. Connors agrees to escape from the institution and help Spider-Man develop a cure for the outbreak on the grounds that he be returned to the asylum when the crisis is resolved. Spider-Man returns to his apartment with Connors, where they immediately set up a laboratory to begin development of the antidote, which soon becomes a race against time when it is discovered that Smythe is developing his own "cure" which involves nanobots destroying the host from the inside out. Along the way, Spider-Man hacks into police and Oscorp transmissions with his Spider-Tracers and forms an alliance with Whitney Chang, an investigative reporter who believes Oscorp's facelift operation is a scam.
Eventually, Connors manages to create an antidote, and Spider-Man rushes it to Gwen and the others at Oscorp; however, Smythe is skeptical that the antidote really works and impulsively uses it on himself. Unexpectedly, Smythe loses both the use of his legs and his mind, and programs his robots to attack Spider-Man in a fit of rage. Narrowly escaping Oscorp and getting back to his apartment, Spider-Man blasts Connors for the imperfect antidote before passing out from his injuries. While he is unconscious, Connors uses his blood to perfect the antidote, realizing that, since Spider-Man is a cross-species himself but retains his humanity, he was the key all along. Upon his recovery, Spider-Man immediately travels to the Oscorp biological labs, where Gwen and the others have been taken to be used as test subjects for Smythe's nanobot "cure," and successfully administers it to Gwen and the others.
With the public at large believing Spider-Man to be responsible for the outbreak, Gwen makes her way to the police station to inform them of the truth, while the CDC quarantines the city with the advancement of the virus, now known as the "cross-species virus." Smythe somehow discovers both Spider-Man's secret identity and where he and Dr. Connors have been staying, subsequently kidnapping Connors and daring Spider-Man to come save him.
Spider-Man breaks into the Oscorp robotics facility and manages to free Dr. Connors, only to be subdued by the robots. While Connors escapes back to his old lab in the sewers, Smythe restrains Spider-Man and injects him with his completed nanobot serum, which strips him of his powers. Despite being severely weakened and assailed by the security robots, Spider-Man escapes the building as Smythe activates his latest S-Bot.
Spider-Man emerges on the streets to discover that the entire city is in chaos as a result of the outbreak. He makes his way to Connors' sewer lab to discover both Connors and Gwen there. With no other way to stop Smythe, Dr. Connors transforms himself into the Lizard again despite Gwen's objections, knowing that he will be able to control himself long enough to stop the robots, while Spider-Man passes out.
Gwen successfully manages to revive Peter, who immediately rushes out to help Connors despite being powerless. Making his way to the S-Bot with the aid of Whitney, Spider-Man, on Gwen's advice, enters the robot and electrocutes himself, destroying the nanobots in his system and regaining his powers. With the aid of the Lizard, Spider-Man successfully disables the S-Bot and subdues Smythe, though Dr. Connors unfortunately loses control of himself to the Lizard's mind in the process. Smythe finally comes to his senses and is left horrified by his actions as he is taken away by the police, while Spider-Man pursues the Lizard into the sewers.
With the aid of a reprogrammed Hunter robot, Spider-Man tracks down the Lizard and manages to transform him back into Dr. Connors, proceeding to take him back to the asylum. Sometime later, Peter and Gwen watch a news report from Whitney Chang, who reveals the "cross-species virus" outbreak has been cured and Spider-Man is now revered by the city for his role in stopping the virus. Whitney subsequently receives news that Smythe has escaped police custody, but Gwen convinces Peter to deal with it later.
In a post-credits scene, Smythe, now able to use his legs again and in the final stages of cross-species infection, makes his way to his underground lab. While walking to his lab, an active hunter bot detects the almost fully developed cross-species Smythe and powers up. The screen fades black
