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A year after the events of Extinction, Alice and her clones travel to Tokyo to find and stop Albert Wesker. They infiltrate his underground base, dispatching several guards along the way before Alice confronts Wesker. During the fight, Wesker injects Alice with a serum that kills the T-virus inside of her, effectively neutralizing all of her superhuman abilities, including her telekinesis. Alice escapes the base, but not before Wesker activates a bomb inside the building which leads to its destruction, and the death of all the clones.

Six months after escaping from Tokyo, Alice travels to Alaska to join the convoy survivors, but only finds Claire Redfield (who has been implanted with a device similar to the one seen on Jill Valentine's chest in Biohazard 5). After its removal, Alice and Claire decide to fly to Los Angeles. They spot survivors that have taken shelter in the Los Angeles Prison that is surrounded by thousands of zombies. Among the survivors are Chris Redfield, Luther West, Bennett Sinclair, Crystal Waters, Angel Ortiz, and Kim Yong. Luther introduces Alice to Chris,who is being held in a cage due to being wrongfully accused that he is a criminal. Chris asks Alice to talk some sense into them because he is innocent, but Alice just ignores this and leaves, but Chris tells her that they're gonna need him because he knows a way out. The barricades around the prison are eventually broken, leading to encounters with mutated zombies. Alice decides to release Chris. After releasing Chris, he is shocked to see that his sister, Claire, still alive. Chris tries to make Claire remember him but she just attacks him. Alice explains to Chris that Claire lost her memory. A battle in the shower room with the Executioner ensues. One by one the survivors are killed with the exception of Alice, Chris, and Claire.

After escaping the prison, the remaining survivors end up on a massive ship off the coast of Los Angeles, where Wesker returns and has a final showdown with Alice, Claire, and Chris. The ship is the Arcadia, the so-called safe place where there is no infection. After boarding it, the group finds over 2,000 survivors and after seeing an Umbrella logo, realize that its an Umbrella trap to capture people to experiment upon. At least some of Claire's memory returns and she remembers that after landing on the beach they were approached by Umbrella men and had the devices put upon their chests, but Clarie fought back and managed to escape but lost her memory as a result of the device. They start releasing the prisoners, starting with K-Mart and Alice, while searching the ship further, encounters Wesker who survived the earlier fight thanks to the T-Virus along with Bennett and two zombie dogs which keep her at bay.

Claire and Chris ambush Wesker and fight him, while Alice retrieves one of her shotguns and kill the dogs, but Chris and Claire are unable to defeat Wesker and are trapped. Wesker tries to eat Alice, but she stabs him in the head with a knife, stunning him and tries to go for her other shotgun. Bennett gets there first, but is knocked out by a recovered K-Mart who tosses Alice back her shotgun, allowing her to blast Wesker's head open and free Claire and Chris. Wesker's powers keep him alive so Claire and Chris empty their pistols into him before locking him and Bennett in a room together and go free the other prisoners. Wesker regenerates and kills Bennett then escapes into a helicopter and activates the purging bomb to kill everyone aboard Arcadia. However, he finds that Alice hid the bomb aboard the helicopter and it is destroyed. During the purging bombs explosion, a parachute falling from the sky goes unnoticed by Alice, Claire, and Chris hinting that Wesker may still be alive.

A mid-credit sequence shows Jill Valentine, wearing a device identical to the one Claire had on her when Alice found her, briefing the soldiers on what they are going to face on the ship and that they are gonna be in the fight of their lives.

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