"They"

What we can surmise about "them" is mostly taken from rumor and the cryptic Arilou. We know that the Androsynth civilization was harnessing their psychic abilities, and was then completely wiped out by an unknown force. The Arilou intimated that this may have been because the Androsynth exposed themselves to "them", and warned The Captain about humans following suit.

The Arilou let on that much of what they have been doing to humans is "changing their smell", whatever that means.