The film opens with Alice (Milla Jovovich) explaining the origin of the T-virus. Dr. James Marcus (Mark Simpson) wanted to create a cure for his daughter Alicia (Ever Anderson), who was suffering from progeria. Marcus created a cure within the Umbrella Corporation, but soon, he would be betrayed by his colleague Dr. Alexander Isaacs (Iain Glen) after Marcus wanted to shut down the program after seeing the devastating effects of the virus. Isaacs has Albert Wesker (Shawn Roberts) suffocate Marcus to death, and Isaacs would later become Alicia's guardian and hold her share of the company. Isaacs created the Red Queen in Alicia's likeness and let the T-virus break out in Raccoon City, and within months, the entire planet would be infected over the next ten years.
Alice is wandering around a rundown city by herself. She finds a pond of water and begins drinking before she is attacked by an infected mutant. Alice kills it and then finds a car. A flying monster swoops down and tries to kill Alice but she gets the car started and drives away. The monster chases after Alice. She gets ahead of it and rides off a ramp to slam into it against a wall. It's still alive, but Alice finds a bomb in the back of the car. She detonates it and blows the monster up.
Alice enters a building and is met by the Red Queen. She knows that Wesker betrayed Alice and the other survivors in Washington. The Red Queen tells Alice that there is an airborne antivirus located within The Hive of the Umbrella Corporation, and she has 48 hours to get there and unleash it, or else Umbrella will launch one last strike against the survivors. When Alice questions why the Red Queen would help her, she points out a mutant behind Alice. Alice kills it.
Alice makes her way toward Raccoon City but is ensnared in a trap laid out by Umbrella mercenaries. They start to attack Alice, but she gets the upper hand and starts kicking their asses and shooting them dead. She tries to take one of their motorcycles, but it only works for Umbrella operatives, so it electrocutes her and knocks her out.
Alice wakes up inside a convoy with with other survivors who have been captured. She is greeted by Isaacs. Alice at first questions how he's still alive after she killed him (in "Extinction") but she realizes she killed one of his clones. Isaacs has Alice's hands tied to the back of the convoy, so she has to run as thousands of the undead are chasing her. She hops back onto the convoy and starts fighting Isaacs' henchmen. Isaacs steps out to take on Alice himself. She chops off his hand so she can take control of the motorcycle and escape.
Alice arrives in Raccoon City and sees that The Hive is on the other side of a massive crater in the ground. She heads on over and is hit by a trap set up by some survivors. She is taken in by Doc (Eoin Macken), Razor (Fraser James), Christian (William Levy), and Cobalt (Rola). They try to hold Alice captive until Claire Redfield (Ali Larter) steps out and sees Alice.
Doc treats Alice, and she learns that he and Claire have formed a relationship. Alice explains her intentions and plan to storm The Hive in order to get the cure.
Isaacs leads the convoy toward Raccoon City with the undead following closely. The survivors gear up for the impending attack. Alice meets Abigail (Ruby Rose), a mechanic that built most of the machinery in the hideout. With her help, the survivors construct traps as the undead start closing in. The survivors launch flaming barrels into the undead crowd, along with sending huge chunks of debris down on them. A female survivor starts running toward the hideout. The group tries to protect her, but Isaacs has her shot dead before she can reach the gate.
The survivors start making their way toward The Hive. Cobalt gets killed by the undead. Alice fights one of Isaacs' henchman, Chu (Joon-Gi Lee). He nearly overpowers her until Alice shoots him. They tie Chu to the back of the convoy, but he's not as fast as Alice and he becomes zombie food.
Isaacs orders Wesker (who's operating from Umbrella's main building alongside the Red Queen) to send out the Cerberus dogs to attack the survivors. Christian is mauled by one of the dogs, and the rest of the group escapes by jumping into the river.
The team heads inside The Hive and are confronted by a now undead Christian. He chases the team into the building as the walls start closing in. Alice fights Christian and gets out before the walls close on him. As they advance further, they encounter a computer with the Red Queen speaking to them.When asked why she is helping them, the Red Queen shows the group a video file of a board meeting in Umbrella with Isaacs deciding that they must go ahead and willingly kickstart the apocalypse and weed out the strongest survivors among them. The Red Queen considers it as going against what she was programmed to do. She tells Alice to take an earpiece so that she may inform her that there is an Umbrella informant among them.
The team must go through a rotating fan. Wesker has it go in reverse, causing the fan to suck the air in the opposite direction and pull the team toward it. Alice grabs Abigail before she gets pulled in, but Abigail loses her grip on the bag she's holding onto, and she gets shredded by the fan.
The team gets closer to their destination. They crawl through some vents which lead to some members falling through trap doors. Alice and Razor fall into a room where Razor gets killed by a mutant beast. Alice shoots it multiple times, but it doesn't die. Alice battles the beast and eventually kills it.
Alice, Claire, and Doc make it to the top floor of the facility to encounter the original Isaacs (the one from before was another clone). Alice considers her options in killing him with an ice pick, decanter, and glass at her disposal, but Isaacs has a protective software in his lens that allows him to anticipate a possible attack. He holds the antivirus and threatens to drop it unless Alice drops her gun. Doc doesn't drop his, and Alice figures he was the informant. Isaacs then reveals to Alice that she was always a clone of Alicia Marcus. With this revelation, the antivirus would kill her since it would destroy anything infected by the T-virus. The original Alicia (also Milla Jovovich) is an old woman in a wheelchair who missed out on life due to her illness. She blames herself for the outbreak because she felt she was too weak. Wesker appears and holds Claire at gunpoint. Since the Red Queen cannot harm an Umbrella employee, Alicia fires Wesker, allowing the system to slam a door down and sever Wesker's foot. Isaacs gets away and Alice leaves Doc to Claire. She shoots him in the head for his deception. Alice leaves Wesker with a detonator in his hand for when he is ready to die.
Alice and Claire go after Isaacs. They fight him as he ascends on a platform. Alice follows him into the laser grid. Isaacs holds her hand and has her fingers severed, but Alice took the opportunity to pull a pin from a grenade in Isaacs' pocket. It blows up on his side. Alice takes the antivirus from his pocket and kicks him down.
Alice goes outside to drop the antivirus as time is about to run out. She drops it but Isaacs catches it. Just then, the Isaacs clone arrives with the undead army. He sees the original Isaacs and is in disbelief that he is not the original himself. Clone Isaacs stabs Original Isaacs to death before the undead tear into the clone. Alice drops the antivirus before the undead catch up to her. Every single one of them drops dead for good. Wesker takes his thumb off the detonator, causing the facility to blow up and kill him and Alicia. Alice then collapses.
Alice wakes up to Claire telling her she succeeded. Alice wonders how she is still alive. A projection of the Red Queen tells Alice that the antivirus destroyed the T-virus cells in her body, but her healthy cells kept her alive. Alice asks why the Red Queen didn't tell her this before, and she states that she needed to know that Alice would be willing to sacrifice herself for the rest of humantiy. She shows Alice that before Alicia died, she uploaded her memories to give to Alice so that Alice may remember the life Alicia used to have now that she is the woman Alicia could never be.
Alice rides away on her motorcycle alone. Her voiceover states that it could take years for the antivirus to completely spread across the globe, and that her work is not done. She is pursued by three winged monsters flying overhead. Alice simply grins and keeps on riding.
*CUT TO THE CHASE*
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The T-virus was originally designed as a cure by Dr. James Marcus for his ailing daughter Alicia to cure her progeria. Dr. Alexander Isaacs betrayed Marcus, killed him, and set the virus loose on the globe.
Alice is told by the Red Queen that there is an antivirus in Raccoon City. She returns to The Hive with a group of survivors to confront Isaacs and Albert Wesker. Isaacs reveals that Alice is a clone of Alicia Marcus, whose image was used for the Red Queen, and who now has the appearance of an elderly woman due to her illness.
Alice fights Isaacs and successfully releases the antivirus, knowing it would kill her because she has T-virus cells in her. Isaacs and Wesker are killed, but Alice survives because she has healthy cells with the T-virus cells gone. She continues to set about the globe to search for survivors.
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