Dark Skyheed is Duke Skyheed transformed like Daxter can do, and like Jak used to do, except Skyheed was not pumped, or doused, he drew massive amounts of Dark Eco to his body.
In this dark form he is seemingly acknowledged by Precursor technology since some defence systems that targeted Jak's ship left Skyheed alone.
Skyheed is presumed dead after the Behemoth is destroyed with him inside of it.