Alice and the others on the Umbrella Corporation freighter Arcadia face an attack by a fleet of tiltrotors led by Alice’s former ally, Jill Valentine. Alice is captured in the attack, while the fates of Chris Redfield, Claire Redfield and K-Mart are left ambiguous.
Alice awakens in an underground facility and is interrogated by Jill. During a power failure, Alice escapes her cell and the laser grid, finding herself in a simulated Shibuya Square, Tokyo. Fighting her way out against zombies, she enters a control room and encounters Ada Wong, one of Albert Wesker’s top agents. Ada explains that they no longer serve Umbrella and the power outage was staged by Wesker hacking into the facility’s computers. Wesker appears on a screen, revealing that the Red Queen now controls Umbrella. Ada explains that the facility is underwater, located in Kamchatka, Russia, that served as a former Soviet naval outpost. The facility was designed by Umbrella in manufacturing clones and created simulated outbreaks to show the effect of the T-virus. Ada and Alice plan to rendezvous with a rescue crew, which includes Leon Kennedy, Barry Burton and Luther West, Alice’s ally which has survived after the outbreak on Los Angeles. Leon’s team plants explosives near the entrance of the facility, which will detonate in two hours to ensure the facility’s destruction. The group plans to meet with Alice and Ada in the Raccoon City suburbia area. In a New York City simulation, Alice and Ada defeat two Axemen. Leon and his team enter a Moscow simulation, but are attacked by armed Las Plagas Undead.
In the Suburban setting, Alice and Ada encounter Becky, the deaf daughter of another Alice clone who mistakes the real Alice for her mother. They also encounter clones of Alice’s former compatriots, the One, Rain Ocampo and Carlos Olivera, who are sent to capture them. Ada gives Alice her smart glasses so that she and Becky can find their way and become split up. They encounter another clone of Rain, who was a friend of Becky’s mother and Alice gives her a weapon. She then rescues Leon’s surviving crew from the barrage of zombies and a giant Licker. Once united, the heroes head for the facility exit but are assaulted by the clones and Becky is captured by the Licker. Alice rescues her, using Leon’s bombs, kills the Licker and allows the heroes to escape; the good Rain clone and Barry are killed during the battle.