Peter's life-long yearning for M.J. becomes even stronger as he fights the impulse to abandon his secret life and declare his love. In the meantime, M.J. has moved on with her life. She has embarked on an acting career and has a new man in her life. Peter's relationship with his best friend Harry Osborn (James Franco) has been overshadowed by Harry's growing vendetta against Spider-Man, whom he holds responsible for his father's death.

Peter's life becomes even more complicated when he is pitted against a powerful new nemesis, the brilliant Dr. Otto Octavius (Alfred Molina) who has been reincarnated as the maniacal and multi-tentacled Doc Ock. Peter must now learn to accept his fate and harness all his superhero talents in order to stop this diabolical madman in his octagonal tracks.