Later, Captain Stacy opens the door to Gwen's room and finds her talking to Peter Parker, whom she had invited to her house for dinner earlier that day. Although they weren't doing anything but talking, Stacy obviously isn't thrilled about the picture, and becomes suspicious about Parker. At dinner, when the topic of Spider-Man comes up, Stacy discusses with his family and Peter about how he will capture the masked menace; Peter defends Spider-Man as "doing something the police can't", and begins to accidentally anger Stacy, further ruining his first impression. However, dinner is suddenly interrupted when The Lizard is spotted rampaging through the Williamsburg Bridge, and Stacy immediately goes out to hunt down the monster.
After Spider-Man saves the lives of several people and fights off the Lizard on the bridge, Stacy's hatred toward Spider-Man remains undeterred, and the next morning, he issues an arrest warrant for "the masked vigilante known as 'Spider-Man'." He continually gets New York's finest police officers to go after him, but to no avail.
Heading back to his office at the NYPD's headquarters, Peter arrives there and tells him that Dr. Curt Connors is going to turn all of New York into powerful man-lizards, and that Stacy has to help him stop him. However, Stacy, who was already disapproving of Peter from the night before, has the cops escort him out of the building, refusing to believe what Peter says. However, after contemplating it, he reluctantly has an officer run everything they have on file about Connors.
After helping clean up the battle between Spider-Man and The Lizard at the school, Stacy resumes the hunt for both of them.
That night, Lizard launches a biological attack on New York City, and while Stacy orders a squad to stop it, Stacy himself instead personally leads a chase on Spider-Man. When Spider-Man is caught in the sight of the police, Stacy's helicopter stuns Spider-Man out of the air. The cops put Spider-Man in handcuffs, but when Stacy pulls off his mask, Spider-Man quickly beats up the cops and is about to escape until Stacy gets up and holds him at gunpoint, forcing Spider-Man to freeze. Realizing the situation, Spider-Man turns around and reveals himself to be Peter Parker. Stunned, Stacy is taken back by the revelation, but Peter convinces him that he has to stop the Lizard before it reaches Oscorp where Gwen is, and Stacy reluctantly lets him go. He then heads over to Oscorp, where he runs into Gwen. He reveals to her that he knows about her boyfriend's secret, and she gives him an antidote that will cure the lizard toxin and pleads him to make sure Peter's okay.
Eventually, Stacy somehow makes it near the top of Oscorp Tower and assists Spider-Man in defeating the Lizard. He gives Peter the antidote from Gwen and buys him time by fighting the Lizard himself. While Peter goes to switch the lizard toxin with the antidote, Stacy fires his shotgun at Lizard, but the monstrous reptile quickly heals from his wounds and attacks the Captain, mortally wounding him. Peter successfully releases the antidote into the air, but falls from the collapsing tower, and is saved by Connors, who is beginning to transform back to his normal form. Peter returns to Stacy, who is bleeding heavily. In his final moments, Stacy tells Peter that he was wrong, and that New York does need Spider-Man. However, he warns Peter that being a superhero will often put the ones closest to him in danger and that it will come with sacrifices. He then forces Peter to promise that he will leave Gwen out of it, so that she is not harmed by Peter's status as Spider-Man. Peter agrees, and mourns as Stacy dies.
Later, Stacy has a funeral where he is honored for his work as New York's top cop, and Gwen notes that everyone, even Flash, shows up, except for Peter. She arrives at his apartment, and Peter tells her that he can no longer be with her, and she realizes that her father made him promise that. The next day in school, the two sadly ignore each other, until, in class, the teacher scolds Peter for being late, and when he says it won't happen again, she tells him not to make promises he cannot keep. Sitting behind Gwen, Peter quietly and slyly replies, "Yeah, but those are the best kind," which causes Gwen to smile, meaning that, for better or worse, Peter is going to stop honoring his promise to Captain Stacy and start dating Gwen again.
George Stacy appears often as a vision and hallucination to Spider-Man, haunting him for the promise he did not and does not keep about his daughter. Gwen's death at the hands of the Green Goblin proved that Stacy was right, because Peter did not keep his distance from her and thus Gwen was killed by Spider-Man's enemy after finding out that Peter was Spider-Man, who also knew Gwen.
- George Stacy was one of the few people to know Spider-Man's true identity before he died. The others are his daughter, Harry Osborn, and Connors.
- He used to believe Spider-Man was a criminal, but later when he found out Peter was Spider-Man, he began to see him as a true hero.