From Data Realms Wiki
These alien robots of unknown origin and age are found dwelling on the moon of the planet. Unfortunately they wake up and show hostile intentions.
Remnants of Mu-ilaak (story only)
Gameplay: These are found on the moon a bit into the story line. They are powerful robots/cyborgs, and can replicate without using facilities aboard a Trade Star. Everyone gangs up on them eventually. Yeah, it's the "united against our common enemy" plot device. In reality FreeTrade wants to get rid of them because they're bad for business.
Analogy: Initially superior, bad guys.
Colors: Red and silver. 
Cortex Command's story mode was cancelled in favor of completing just the campaign mode after 11.5 years of development. The intention was that the Remnants of the Mu-ilaak would be "the big bad". Your heroic ally would be Uzira, an early human explorer who went into cryogenic sleep after an inconclusive last battle with the Mu-ilaak which left both sides exhausted and stranded on the planet's moon.
Official concept art show the Mu-ilaak to feature a detachable "mosquito-like" units fans have called a headcrab, as it appears to play a role in taking control of bodies like the "interrogated human" pictured. It also is depicted rebuilding a body which appears to have decayed to bare bones.
As speculation, fans have considered Mu-ilaak capable of regenerating their own bodies if the head remains intact, and possibly of converting living or dead bodies of other species into Mu-ilaak drones.
The Mu-ilaak are depicted with firearms featuring a prominent downward extension from the muzzle, which appears somewhat on the "chin" of the mosquito headcrab and the interrogated human. Mu-ilaak weapons may be plasma based, judging only from the color and shape of projectiles in an official drawing of a Mu-ilaak fighting Uzira's skeleton forces. The weapons appear to be mostly silver-grey with some green accents.