The Alice clones (Milla Jovovich) attempt to kill Albert Wesker (Shawn Roberts) at his base in Tokyo. The clones are killed by a bomb, activated by Wesker as he escapes the facility in an aircraft. The original Alice ambushes him, but Wesker injects her with a serum that neutralizes the T-virus, eliminating her superhuman powers. He reveals that his T-virus powers have surpassed her own, but before he can kill her, the aircraft crashes and Alice escapes from the wreckage.
Six months later, Alice commandeers an airplane to follow emergency broadcasts from a safe haven known as "Arcadia" in Alaska. Alice hopes to find her friends Claire Redfield (Ali Larter), K-Mart (Spencer Locke) and others, but has yet to find any sign of human life. At Arcadia, she discovers the helicopter her friends used, and is then attacked by a crazed Claire, controlled by a device attached to her chest. Alice removes the device; as Claire recovers, it becomes clear that it has damaged Claire's memory.
The two fly to the ruins of Los Angeles and find a group of survivors living in a prison, surrounded by zombies. Luther West (Boris Kodjoe), a former basketball star and celebrity, leads the small band: Wendell (Fulvio Cecere), aspiring actress Crystal Waters (Kacey Barnfield), film producer Bennett (Kim Coates) and his intern Kim Yong (Norman Yeung), and Italian expatriate Angel Ortiz (Sergio Peris-Mencheta). With their help, Alice lands her plane on the roof of the prison and learns that Arcadia is not a fixed place but actually a cargo tanker traveling along the coast. Instead of attempting to fly her new friends to it one by one, Alice and the survivors decide to find an alternate means to make it to the Arcadia. This route takes the form of a prisoner Chris (Wentworth Miller), who was found locked in a maximum security cell. He says that he is a soldier who was locked up by prisoners as a cruel joke. He claims that he knows a way to escape the facility, but will not reveal it unless he is released.
The issue is forced with the advent of "Majini" zombies, who tunnel into the prison via the sewers and kill Wendell, and the Executioner, a giant axe-wielding monster who assaults the front gate. Chris reveals himself as Claire's brother, but she does not remember him. The group splits into three: Alice, Chris and Crystal raid a hidden arsenal, Crystal is killed by the zombies during the raid; Luther and Claire attempt to reinforce the gate; and Bennett, Angel and Kim Yong ready a hidden infantry fighting vehicle, Chris' proposed escape route. Unfortunately, its engine was removed for maintenance; when Bennett discovers this, he shoots Angel, commandeers Alice's aircraft, and escapes. The remaining quintet are forced to escape down the sewers. Kim Yong is killed by the Executioner, whom Alice and Claire then defeat. The group lose Luther to a cave-in.
Alice and the Redfields commandeer a boat and board the Arcadia, finding it functional but abandoned, even though the manifest lists more than 2000 survivors on board. As they explore, Claire recalls what happened to her group when they arrived in Alaska: Umbrella ambushed them and attached the devices to them, with only Claire managing to escape. She concludes that the ship is a trap, meant to lure survivors in for further experimentation. The trio begin releasing survivors, among them K-Mart, while Alice discovers a blood trail and continues deeper into the ship. She finds Wesker, who explains that the T-virus gave him incredible powers, but that he is constantly at war with the T-virus for control. In order to pacify it, Wesker regularly ate fresh human DNA, scaring the Umbrella employees into deserting the ship. He hopes to gain control of the virus by eating Alice, the only individual to bond successfully with the T-virus on a cellular level.
Chris and Claire arrive and attack Wesker while Alice battles two dogs and Bennett. Wesker easily overpowers Chris and Claire, but Alice is able to defeat him with help from K-Mart. Wesker regenerates and escapes by aircraft, activating the bomb on the Arcadia in an attempt to destroy the ship and kill the remaining survivors but, anticipating these actions, Alice had hidden the bomb aboard his plane, which explodes as everyone watches from the deck of the ship. Unknown to them, a figure parachutes away from the explosion unnoticed, while Luther emerges from the sewers, battered but alive.
Alice resolves to turn the Arcadia into a real safe haven and broadcasts its message for any other survivors. As Claire, Chris, and Alice decide how to proceed, they see an approaching Umbrella assault helicopter squadron led by Jill Valentine (Sienna Guillory), who is under the control of the same Umbrella device used on Claire.
