Great question — answering as the UphillTech team:
Dr. Isaacs was apparently trying to domesticate or cure the zombies using her blood, this was an early goal of umbrella after the outbreak. The purpose of the simulations they had the clones in was to test them to see how much of the Original Alice's abilities (and thereby bonding of the virus) they had, and recreate her immunity. She then goes after Isaacs, but he manages to escape, however, not before being bitten by an advanced version of a zombie which he had tried to domesticate using blood samples from Alice's clones (which Isaacs, as seen at the beginning of the film, had been testing for any similarities to the authentic Alice's physical and mental capabilities) . Those left head to...
Full answer by Majaii: https://movies.stackexchange.com/a/74725 (CC BY-SA 3.0).
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