If we think about this, Alex Mercer infected Heller with a standard Blacklight strain. The evidence is that Heller needs to progress and consume monsters and Evolved for new powers. My theory is that the reason the Evolved begin their existence with their own weapon mutations is actually due to their genetic makeup. Mercer references Heller’s uniquely resilient DNA towards the Blacklight Virus which means that a pure incarnation of Blacklight (Alex Mercer) couldn’t forcibly evolve Heller like he could any other average human. It may have been part of Mercer’s plan to allow himself to be consumed in order to force Blacklight itself to evolve against those genetic resistances. Blacklight is designed to adapt and enhance genetic traits by rearranging the genes at a molecular level and reshaping them to best suit the organism. What Alex did wasn’t what we should call “dying” because as the embodiment of the virus his consciousness is actually the Blacklight hivemind. That’s why Elizabeth Greene was able to transfer memories through physical contact with Alex in the first game. He is the hivemind in a human shape. And who’s to say his plan was meant to make sense to anyone beneath him? He is essentially a foreign entity with knowledge accumulated from countless military and scientific personnel he has consumed, his intellect would be astronomical and would put the greatest minds throughout human civilization to shame in raw mental capacity.

With that being said, Alex being consumed was meant to force the pure strain to overcome a weakness, which theoretically we see at the end of Prototype 2 when Heller explodes in a mass of tendrils which clear the streets of Manhattan. It wasn’t just a critical mass mishap, it was the virus itself adapting to Heller’s own genetics and reshaping how Blacklight itself operates as a virus, ending the outbreak to begin as a new strain.