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In the weeks and months following the 2002 destruction of Raccoon City, the T-virus has successfully spread across the world. The virus proves to be fatal to many organisms, and mass-desertification has taken place. With the Undead always migrating in search of food, human refugees have long since abandoned their cities in favour of mobile convoys, keeping away from them as long as possible.
Alice drives alone by motorcycle past the city limits of what was once Salt Lake City, now consumed by the expanding Mojave Desert. Having received a radio broadcast from survivors at the local KLKB station, Alice stops to investigate. Finding the woman who made the call - "Ma" - Alice realises too late this is a trap, and the radio station is in fact under the control of bandits who lure survivors to their doom. Eddie (Rusty Joiner) threatens Alice with his kukri and prepares to rape her, but is summarily kicked in the head, killing him instantly. Knocked out in retaliation, Alice wakes up in arena created by the bandits, where she is forced to find their Undead dogs for entertainment. Alice is able to best the dogs, with one getting out and killing Ma, Runty, Piggy, Pock Mark and Rancid. Leaving the dog be, she explores the rest of the station and finds a journal which details a route to Alaska, which the writer believed to be virus-free.
Dr. Alexander Isaacs has been trying to reproduce/clone Alice's powers by creating clones of her, but none of them survive the tasks they are faced with (a mock-up of the mansion, the Hive and Raccoon City Hospital). He concludes to Wesker and the other Umbrella board members that he needs the original Project Alice in order to obtain her blood and hopefully find a mass cure for the virus after discovering that the Undead hunger for flesh yet gained nothing from it. Wesker and the Umbrella board members thus made this together with the capture of Alice among their highest priorities. Using her clones' blood as a basis for the cure, he plans to domesticate the Undead with his newly developed serum harvested from Alice's blood. Initially, the Super Undead displayed signs of heightened intelligence, increased memory power and reasoning skills, but soon grew to be stronger, faster, and more vicious. Isaacs uses this to his advantage by secretly creating a larger group of these 'Super Undead', defying Wesker's orders.
At the same time, Carlos Olivera and L.J. Wayne have joined a convoy of survivors, consisting of K-Mart, Otto, Mikey, Chase Liam and Betty led by Claire Redfield, moving in search of supplies. While searching a motel, L.J. is bitten but doesn't tell anybody. At morning, the convoy is waken up by thousands of infected, hungry crows. When everything seems lost, Alice arrives and using her telekinesis manages to save the convoy. Despite her efforts, Betty, Otto and five others died in the attack.
She tells the group about her plan to Alaska, and they decide to follow it by popular vote. However, before trying the long journey they need supplies, and they decide to search the nearby Las Vegas, now in ruins. Meanwhile, Dr. Isaacs has been looking for Alice, hoping her DNA could be the source for a cure; he finally manages to track her by satellite, but only by a 62% confirmation. He later reports this to Wesker, who instead refuses to have Isaacs recapture Alice until the satellite confirmation hits 100%, but Isaacs is later revealed to have recorded Wesker's speech and edited it to make it appear as if Wesker ordered his second-in-command, Captain Alexander Slater, to send a force to capture Alice. Isaacs then sends a group of his newly created Super Undead to Las Vegas, both to test their ability and capture Alice.
The convoy is attacked by the Super Undead, and most of its members are killed; L.J. eventually succumbs to the T-virus and bites Carlos before being shot dead, Mikey was devoured by a band of Super Undead, and Chase falls from his sniper position in the Eiffel Tower replica while fighting with the Super Undead who managed to locate his position. Dr. Isaacs tries to control Alice via satellite, but she is powerful enough to hack Umbrella's computer network and find out that Isaacs is just a few meters away on the roof of a nearby building. She attacks the few Umbrella men and kills all of them but Isaacs, who manages to escape by helicopter after being bitten by his own creatures.
The few survivors decide to raid a nearby Umbrella facility, hoping to use their helicopter to fly to Alaska. Inside the underground laboratories, Isaacs tries to save himself by injecting more and more antivirus, but he seems helpless and begins to exhibit signs of mutation as a result of the overdose. His second-in-command, Captain Slater, was sent by Wesker to kill him due to his failure and insubordination, but Isaacs proves resistant to gunfire and kills Slater and some nearby guards with his new tentacled hand. He then begins to kill everyone in the base, but he's trapped inside the lower levels by the White Queen, the computer which controls the facility.
The convoy arrives to the facility, only to find out that its perimeter is surrounded by thousands of undead. Carlos, believing his infection to be beyond any cure, chooses to sacrifice himself in order to open a safe path for the rest of the convoy to pass through. He gets into a gasoline truck with some dynamite, drives into the crowd and detonates the explosives. Claire, K-Mart, Liam and the remaining surviving convoy members gets into the chopper and flies away to Alaska, leaving the convoy's fate open to viewers. Alice, meanwhile, decides to get her revenge on Umbrella.
When she gets into the labs she is told by the White Queen, who confirms that the real Alice's blood is the ultimate cure for purging the world of the biohazard, that she has to reach to lower level in order to create a cure. Down there, she finds one of her clones, but before she can examine it, Isaacs now a Tyrant, attacks her. She stabs him with a knife and he flees and is able to instantaneously heal his stab wound. The clone wakes up, seemingly dying in Alice's arms. A battle of telekinetic powers then continues inside the Mansion, and in the replica of the laser corridor from the Hive. Isaacs taunts Alice, saying that he is the "future", with Alice retorting to Isaacs they are both going to die, and the laser cuts him into pieces, but stops just before reaching Alice. Her clone is revealed to have been the one to turn it off.
In Tokyo, Wesker informs the rest of Umbrella that contact with the North American branch has been lost, and decided to control further experimentation from his Japan facility. Using their holographic technology, Alice joins the meeting and informs them that she is after them and "bringing a few of her friends". The film ends as Alice, next to one of her clones, watches hundreds of others awaking.
