Underneath Raccoon City exists a genetic research facility called the Hive, owned by the Umbrella Corporation. A thief steals the genetically engineered T-virus and contaminates the Hive with it. In response, the facility's artificial intelligence, the Red Queen, seals the Hive and kills everyone inside.

Alice awakens in the bathroom of a deserted mansion with temporary amnesia. She dresses, checks the mansion, and is tackled by an unknown person as a group of commandos led by James Shade breaks in. Alice's attacker is cuffed and then released when he claims to be Matt Addison, who just transferred as a cop in Raccoon P.D.