Spider-Man finds Doctor Octopus in the abandoned warehouse on the waterfront, where he's restarted his fusion experiment. Upon seeing Spider-Man there, Octopus concludes that Osborn couldn't bring himself to kill him and engages him in a battle. During their fight, Mary Jane tries to smack Octopus, but he knocks her away. As they fight, the fusion reactor grows more and more and starts dragging every magnet of New York City towards itself, like cars.
After battling with Doctor Octopus, Spider-Man manages to stun him with an electric shock. Peter then reveals his true identity to Octavius and pleads with him to stop the machine as the mechanical tentacles try to strangle him, reminding him how he taught him that intelligence is a gift and that they must use it for the good on mankind, even convincing him to sacrifice the experiment despite it being his dreams by telling him that sometimes people sacrifice their dreams for the greater good (a callback to a conversation he had with Aunt May when she told him about how much Spider-Man's heroism meant for other people). Returned to his senses by the shock and determined to end his doomsday experiment before it causes more harm, forcing his arms to listen to him, Octavius tells Peter that the fusion reactor can't be shut down anymore and that the only solution is to sink it. Spider-Man tries to go to do so, but Ottto stops him, insisting him to let him do so. Octavius proceeds to use his mechanical tentacles to collapse the floor of the building, successfully drowning the fusion device at the cost of his own life, declaring that he would not die like a monster. In the end, as Spider-Man rescues Mary Jane and they escape from the warehouse, Otto drowns in the river along with the sinking fusion core, whilst the river water also shuts down the tentacles and the manipulative advanced AI that corrupted Octavius' mind playing on his vanity and ego all along, allowing him to not die like a monster and precluding his tentacles from doing any more harm ever again.