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Mitochondria Eve has a similar case to the Blacklight Virus.
Somehow, before his death by Blackwatch, Alex has transferred his files about his work to Dr. Hans Klamp. He has instructed him to infect someone with the virus to a perfect and that is Maya Breda. The next instruction is to implant donors to two individuals who will carry on the infection if Maya dies: Aya and Melissa.
The stinger ending of the first game was a good thing.
General speculation is that Aya and then everyone else at the Met had glowing eyes because Aya was losing control of her powers/becoming more like Eve, or Eve was spreading/returning despite Aya's effort. But what if instead Aya was inoculating those around her, so that if Eve or another similar entity appeared, some people would be protected.