While the Black Cat tries to wrangle the remaining Spidey doppelgangers let loose upon the city of New York, Spider-Man confronts their "father," the insane Calvin Zabo--and his monstrous alter ego Mr. Hyde--in his subterranean stronghold. At stake are not only the lives of the homeless youths Zabo kidnapped, but also the life of one of Peter Parker's students, Jordan Harrison, who is mutating into something...inhuman!
Calvin Zabo is seen ingesting his formula and transforms into a huge brute. Mr. Hyde is the "evil" aspect of Zabo. He is now ready to face Spider-Man who is still searching in the sewer tunnels. His tracking device put together by he and Reed Richards tells him that he is close to tracking another created version of him. He finds a structure with several rooms that have a one-way mirror. Spider-Man comments how it appears as if they were like exhibits in a zoo. All of the rooms are empty except for one. To his surprise, he recognizes the occupant as Jordan, one of his former students.
Jordan Harrison doesn't fit the profile of the others. He wasn't homeless but tells Spider-Man that Zabo killed his mom. He also said he'd kill his girlfriend if he didn't go with him. Spider-Man tries punching the glass but it's a special unbreakable kind. He slams against it with his shoulder but doesn't help either. His spider-sense go off as a shadowed figure approaches. Spider-Man must now face Mr. Hyde.
The Black Cat brings in another kid that was given Spider-Man's powers to the police. Detective Fogg tells her that if she happens to run into him, she could give him a message. Not wanting to admit she knows how to contact a wanted fugitive, she cautiously listens. The Detective tells her that there is at least one more kid out there. He then takes her into a room where Jordan's mom and girlfriend are. It turns out Zabo didn't kill her.
Hyde lunges towards Spider-Man, who jumps over him at the last minute. Hyde's blow put a crack in the unbreakable glass in Jordan's holding cell. As they smash through walls, Spider-Man tries to distract Hyde to get him away from Jordan. Spider-Man shoots webbing on Hyde's eyes. He says he embraces pain and begins tearing off the webbing, including his eyelids. He tells Spider-Man that he believes doing evil is as valid of a choice as doing good. He's embraced his dark side. Looking at Spider-Man's black costume, he asks if he's embraced his also.
Jordan, using some physics, applies pressure to the indestructable glass' flawed pressure point. This causes the glass to shatter. Escaping from his room, Jordan finds another room filled with chemicals. He recognizes that they are dangerous.
Hyde and Spider-Man continue to fight. Spider-Man is getting annoyed because he'd rather be by Aunt May's side in the hospital. Hyde mentions that he is aware of her condition. He says the entire underworld knows.
Jordan apprears carrying a flask of chemicals. He says that because Hyde killed his mom, he deserves to die. Hyde seems pleased at Jordan's resourcefulness. He raises the flask and prepares to throw it. Spider-Man recognizes the darkness inside of Jordan. He shoots a web as Jordan is about to throw the chemicals.
Later, Spider-Man is telling Black Cat what happened. Jordan had poured hydrogen fluoride, a deadly acid into the flask. He was able to hit it with his webbing but some still splashed onto Hyde's face. His face was almost completely burnt off and blinded him. It took some blows, but Spider-Man was eventually able to render Hyde unconscious.
It seems that there was a happy ending but Spider-Man notes that Jordan has been affected. He knows how close he came to killing Hyde. He embraced the darkness and will now have to live with it for the rest of his life.