I played it was a child so I don't remember all the details. The game was a 2D side-scroller for the PC. The game was likely released in the late 1990s or early 2000s. You played as a man, and an alien parasite or symbiote infected you. There are a lot of small-cut scenes about this alien inside the main character. I think there is one of the alien sitting on a blood cell, like it is a La-Z-Boy and watching your actions or something. The FBI or some 3 letter agency hunts you early on, but it seems like aliens invade and then your character mutates because of the parasite?