[[WMG:Mitochondria Eve has a similar case to the [[VideoGame/{{Prototype}} 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 [[spoiler:Maya Breda]]. The next instruction is to implant donors to two individuals who will carry on the infection if [[spoiler:Maya]] dies: [[spoiler:Aya and Melissa]].
[[WMG: 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.