The full plot of Resident Evil: Extinction follows Alice and Claire's convoy from the desert to Umbrella's underground facility, where Alice defeats a mutated Dr. Isaacs. After the crow attack, Alice persuades Claire to head for Alaska, and the convoy follows her lead.
Meanwhile, Dr. Isaacs, who is breeding a new kind of zombie, sends his creations to ambush the convoy. He does this against Wesker's orders. Most of the convoy dies in the attack, and L.J. finally turns and bites Carlos.
What is the plot twist in Extinction? There are two. The first is that Alice breaks free of Umbrella's remote control. The second is that the White Queen tells Alice her blood could cure the T-virus, which explains why Umbrella keeps cloning her.
Alice and K-Mart track Isaacs to the company's underground facility. At the entrance, Carlos sacrifices himself by driving a tanker loaded with dynamite into the zombie horde, which clears the way. The others escape by helicopter, but Alice stays behind to finish the job. Inside, Isaacs has mutated into a Tyrant, and Alice lures him into a replica of the Hive's laser corridor and defeats him.
The film then moves to Tokyo, where Wesker learns that the North American facility is lost. Alice appears at the meeting.