Alice wakes up disoriented in a mansion. Wandering through its halls, she is forced to escape several security traps. However, she is eventually killed by a bouncing mine hidden in the floor. Her body is dumped into a pit filled with dozens of Alice copies and is revealed to be one of many clones being produced inside of an underground facility whose entrance above ground is surrounded by thousands of zombies.
Despite the best efforts of the biotech company Umbrella Corporation to cover up the contamination of The Hive and the release of the T-virus to the surface, going so far as to authorize the bombing of Raccoon City, the T-virus has spread around the world. As the virus spread, it affected not only humans, but other animals as well, and the environment deteriorated, turning cities into desolate landscapes and the wilderness into wastelands. The real Alice (from whom the clones are made) wanders the wastelands of the Southwestern U.S. On her travels, she finds a dead man’s diary which states that there is an uninfected area in Alaska. She later begins to realize that she has developed telekinetic abilities due to the experiments performed on her.
Meanwhile, Dr. Alexander Isaacs, former head of Project Alice and the head of the North American Umbrella facility seen earlier (based in Nevada), considers Alice’s recapture to be a top priority since she has the ability to bond with the T-virus and not suffer mutation. He tries to persuade the Umbrella board, operating via holograms from the worldwide Umbrella facility, that he can use her blood to develop a permanent cure as well as tame the infected zombies. The new Umbrella chairman Albert Wesker orders Isaacs to use the clones to create a cure, and he refuses to authorize Alice’s recapture until they are informed of her location.