People who fled the collapse of the golden age during the first attacks of the Darkness took shelter in massive colony ships hiding out in the asteroid belt where they were exposed to a mysterious power in deep space. As to what that "power" is one can assume its the Light of the Traveler reaching out to them from Earth only warped by the Darkness somehow causing them to gain bio-luminescence which is the glowing eyes and light flowing through their skin. Thats what i got from the Grimoires and in game descryption, lol i love my Awoken Hunter, shes a Dead Orbit mercenary which to me made sense in the lore of the game (Dead Orbits leader is an Awoken and they want to spread out to the stars!).