Ock, having restored his project, needs tritium for his reactor, and goes to Harry to get it. Harry agrees to give Octavius all the tritium he possesses in exchange for bringing Spider-Man to him, and tells him that Peter, who is supposedly good friends with Spider-Man, is the key to finding him; however, he tells Ock not to harm Peter. Ock finds Peter and tells him to find Spider-Man, and abducts Mary Jane in the process. Determined to bring her back, and realizing that his powers are restored, he dons his costume again after stealing it from the Bugle, while a furious Jameson continues to denounce Spider-Man as a menace. Spider-Man meets and battles Ock, where they fall onto a passing train. Ock increases the train's throttle to full, then disables the controls and jumps off. With great effort, Spider-Man manages to stop the train before it can plunge over the end of the track. The passengers see him unmasked for the first time and realize that he is just a young man; in gratitude, they promise never to tell anyone. Suddenly Ock returns, knocks Spider-Man unconscious and delivers him to Harry.
After giving Ock the tritium, Harry prepares to kill Spider-Man; he falls back in shock to discover that Spider-Man is Peter himself. Peter convinces Harry to reveal Ock's whereabouts and makes his way to his waterfront laboratory. Although Spider-Man attempts to rescue Mary Jane discreetly, one of Ock's tentacles senses him and they fight once more. Spider-Man ultimately subdues Ock and reveals his identity to him, and convinces him to let go of one's own ambitions for the benefit of the greater good. Octavius finally relents and commanded his tentacles to obey him; he decides to drown the fusion reactor into the Hudson River to prevent it from leveling the city, taking his own life in the process. Mary Jane finally learns of Spider-Man's true identity, and understands that as long as he is Spider-Man, she and Peter cannot be together. Spider-Man returns Mary Jane to John and leaves. Meanwhile, Harry, still traumatized by what he witnessed, is suddenly visited by the ghost of his father in a hanging mirror, pleading him to avenge his death. Enraged, Harry shatters the mirror, revealing a secret room containing the Green Goblin's equipment (which Peter hid after his death), pondering what to do next. Mary Jane, on her big day, changes her mind in marrying John and arrives at Peter's apartment. She tells Peter that she loves him and wants to be with him no matter what. After a passionate kiss, a siren is heard and Mary Jane encourages Peter to respond as Spider-Man, quietly apprehensive of the dangers they are about to face as a couple.