Peter Parker, portrayed by Tobey Maguire, has finally reached a point of stability in his life and is ready to propose to his beloved Mary Jane Watson, played by Kirsten Dunst, who recently made her debut on Broadway. However, during a romantic outing, disaster strikes when a small meteorite crashes nearby, bringing with it an alien Symbiote that attaches itself to Peter's moped. In a parallel storyline, the escaped convict Flint Marko, embodied by Thomas Haden Church, is on the run from the authorities and falls into a particle accelerator. This accident melds his body with sand, granting him the sinister ability to shapeshift, thus transforming him into the formidable Sandman.
Compounding Peter's challenges is his best friend, Harry Osborn, played by James Franco, who is driven by a desire for revenge against Peter, whom he blames for his father's demise. Harry unleashes a series of attacks using dangerous weaponry derived from his late father's Green Goblin technology. In a twist of fate, Harry suffers a head injury during this conflict, resulting in partial amnesia that erases his memories of their feud and his knowledge of Peter's secret identity.
As the story unfolds, Peter attends a festival honoring Spider-Man for saving Gwen Stacy, portrayed by Bryce Dallas Howard. At this event, Sandman attempts a brazen robbery, overpowering Peter in the process. Following this altercation, NYPD Captain George Stacy reveals to Peter and Aunt May, played by Rosemary Harris, that Flint Marko was responsible for Ben Parker's death, and that Dennis Carradine was merely an accomplice.
Fueled by revenge, Peter seeks out Marko. As the Symbiote fuses with his suit at night, he awakens with enhanced powers and a darker personality. This new suit influences him negatively, as he becomes increasingly selfish and arrogant. In an intense confrontation with Marko in an underground subway tunnel, Peter discovers that water can dissolve the Sandman and unleashes a torrent, seemingly annihilating him.
However, Peter's drastic personality shift alienates Mary Jane, who struggles with her own career setbacks. Finding comfort in the company of Harry, their relationship intensifies when Harry regains his memories and pressures her to end things with Peter. After Mary Jane breaks up with him to pursue another relationship, Harry escalates their rivalry, only leading to a climactic confrontation at the Osborn estate.
In a fierce battle fueled by the Symbiote's corrupting influence, Peter emerges victorious, but at a heavy cost. As he ruthlessly humiliates Eddie Brock, played by Topher Grace, a rival photographer who falsely portrays Spider-Man as a criminal, he inadvertently pushes Eddie to the brink. J. Jonah Jameson, portrayed by J.K. Simmons, fires Eddie after discovering the deception, leaving him in a seething rage.
Desperate to make Mary Jane envious, Peter invites Gwen to the nightclub where Mary works, leading to a series of tragic misunderstandings and ultimately ending in a disastrous confrontation between Peter and Mary Jane. Realizing the destructive impact of the Symbiote on his character, Peter seeks to rid himself of it. Arriving at a church bell tower, he finds that the bell's sounds weaken the Symbiote, allowing him to remove it successfully. However, in a serendipitous turn of events, the Symbiote falls onto Eddie, transforming him into the formidable Venom.
The newly formed duo, Sandman and Venom, colludes to capture Mary Jane, endangering her life and forcing Peter to unite with Harry once more. Together they face a menacing battle against their foes. Tragically, Harry sacrifices himself to save Peter, mirroring his father's heroic fate. Although Peter and Harry reconcile before the end, their victory comes amidst great loss.
After defeating Venom and Sandman, Peter learns that Flint Marko did not intend to kill Ben Parker; it was an accidental tragedy spurred by desperation to save his dying daughter. In a poignant moment, Peter forgives Marko, who fades away, while he and Harry share a final understanding before Harry's passing. The story concludes with Peter attending Harry's funeral, alongside Aunt May, Bernard, and the Stacys, before reuniting with Mary Jane in a jazz bar, where they begin to dance and mend their fractured relationship.
