The full plot of Resident Evil Apocalypse runs from the quarantine of Raccoon City to Alice waking in an Umbrella lab, where Dr. Isaacs reveals that her escape was part of Umbrella's plan. Alice and Matt escape the Hive, but Umbrella captures them and the T-virus gets loose in the city. Umbrella quarantines Raccoon City, and Major Cain seals the exit bridge, trapping the living and the undead together.
Alice, now enhanced by the virus, joins former police officer Jill Valentine, soldier Carlos Olivera, reporter Terri Morales, L.J. and others. They agree to find Angela Ashford, the daughter of Dr. Ashford, in return for a safe route out of the city. Dr. Ashford's research led to the T-virus, which was originally meant to treat his daughter's genetic condition. Angela explains that an antivirus exists that can stop the infection, and Alice uses it to cure Carlos.
Umbrella then releases Nemesis, a huge engineered soldier, to kill the survivors and test his abilities. At the extraction point, Cain kills Dr. Ashford and forces Alice to fight Nemesis. Alice wins but stops when she realizes he is Matt. Nemesis turns on Cain's troops and dies protecting her. The survivors take the helicopter and throw Cain out to the zombies.
A nuclear warhead then destroys the city, and the blast brings the helicopter down. Alice shields Angela and is badly impaled, while news reports blame a power plant meltdown and hide Umbrella's role. Alice wakes in an Umbrella lab and escapes with Carlos, Jill, L.J. and Angela, and Dr. Isaacs reveals that her escape was part of Umbrella's plan.