Tuurngait

The Tuurngait is an extraterrestrial entity that uses its powers and intelligence to transform the sanest, smartest humans on Earth into mindless, flesh eating zombies.

History
Long before the arrival of the Archaic, the Tuurngait was worshipped by the Inuit, who believed it to be a benevolent spirit. However, once it was disturbed by the Archaic researchers, it spread itself through the ranks of the Shelter and turned them into husks that housed the Tuurngait's will within them. It informs Phillip at the end of Black Plague that it wishes no harm to humans, only wanting to be left alone. However, there are no signs that the Archaic actually wished harm to the Tuurngait, despite its claims to the contrary, and the notes found by the player all state that the Tuurngait virus was unleashed immediately after the discovery of the ruins.

This means that it's very possible that the virus was attempting to manipulate Phillip, which would explain why the monsters attempt to kill him throughout the series, despite the Tuurngait's statements that it wishes no harm. Left unexplained are the reasons that the Tuurngait felt it neccessary to kill Clarence instead of simply reintigrating him, or why the animals in the game were of lesser intelligence, according to Howard. The worms and spiders aren't explained either, but it seems likely that they were infected by the Tuurngait far earlier than when the Archaic set up shop there and mutated over time to fit its needs. Lastly, at the end of Black Plague Philip seems to be succumbing to some form of infection, despite the Tuurngait's assurances that he was 'stronger' than Howard.