Claire Redfield and her brother Chris are children living at the Raccoon City Orphanage. Claire meets and befriends Lisa Trevor, a disfigured girl who has been experimented on. Dr. William Birkin, an employee for the Umbrella Corporation, oversees the orphanage and takes children for his own experimental research. Claire escapes from Birkin when she is selected to participate in an experiment.
In 1998, Claire returns to Raccoon City, hitchhiking in a semi-truck. While distracted, the truck driver hits a woman who is walking in the road. When Claire and the driver investigate, the woman disappears, leaving only a pool of blood behind. The truck driver's Dobermann licks the blood, and, over time, begins to foam at the mouth; becoming erratic. Meanwhile, Leon S. Kennedy, a rookie police officer, notices that the diner's owner has blood coming from her eyes when a deformed crow crashes into the window.
Claire heads to Chris's home to warn him about Umbrella's experiments, revealing Ben Bertolucci as her source of information. After Chris leaves for the police station, Claire steals his motorbike. Before leaving, a child breaks into the house, running from his mother; both have severe hair loss, are erratic, and bloody.
At the police station, the STARS Alpha team meet with Chief Brian Irons to discuss the recent events. Irons explains he doesn't know what is going on, but that Bravo team is missing while investigating a death at the remote Spencer Mansion. Alpha team, composed of Chris, Jill Valentine, Richard Aiken, Brad Vickers, and Albert Wesker is sent to the mansion to investigate. Traveling by helicopter, Alpha team find Bravo team's police vehicle and follow tracks to the mansion.
Inside, the team splits up with Wesker and Jill going upstairs. Unknown to his teammates, Wesker is an operative for an unidentified party, tasked with stealing Birkin's virus, using inside knowledge to navigate the mansion. Jill then sees the helicopter crashing into the mansion, after the pilot Brad gets bitten by a zombie. Wesker saves Jill from another zombie before leaving the team. Meanwhile, Chris and Richard encounter zombies eating the bodies of Bravo team. Richard is eaten while Chris battles the horde, with Jill ultimately saving him. The pair flee the zombies, following Wesker into a secret passage he unlocked.
Back at the police station, the truck driver, now bitten by his dog, transforms into a zombie and crashes his truck into the entrance of the station. Chief Irons shoots the aflame zombie, awakening a sleeping Leon, then announces he is leaving, putting Leon in charge. Irons travels out of the city, but is stopped by Umbrella guards who shoot civilians attempting to escape the city. Returning to the station, Irons is attacked by a zombie dog but Claire rescues him. Claire and Leon retrieve weapons and supplies from the armory and encounter Ben.
Hysterical, Ben steals Leon's gun, but a zombie inmate bites him before he is able to escape his cell. Leon, Claire, and Irons then abandon the police station and travel to the Orphanage, looking for a secret Umbrella tunnel in the building. A licker kills Irons and attacks Leon, but he is saved by Lisa who recognizes Claire and gives them the keys to the secret passage.
Wesker, traveling through the passage, encounters Dr. Birkin. Birkin reaches for his gun shooting Wesker in the chest before Wesker shoots back, nearly killing him. Birkin's wife Annette then grabs the gun, but Wesker shoots her and kills her. When Wesker hesitates to pull the trigger on Sherry, Jill shoots him. Chris rushes to Sherry and finds that William has injected himself with the "G-Virus", who begins mutating. Chris, Sherry, and Jill run from Birkin, reunite with Claire and Leon and escape to an underground train. The train is stopped when Raccoon City is destroyed, allowing a fully mutated Birkin to attack the train. Leon saves Claire by shooting him with a rocket launcher, killing him.
In a mid-credits scene, Wesker awakens in a body bag, unable to see anything. A figure then hands him sunglasses and reveals herself as Ada Wong.
