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. Alice and Matt are ordered to go down to the Hive with the group, where they find another amnesiac, Spence, hidden in their train. The commandos explain that everyone in the group except Matt is an employee of the Umbrella Corporation, and Alice and her partner Spence were assigned to guard the Hive’s secret entrance under the mansion.