These enemies are manufactured by Dr. Proton on Area 51 in order to destroy the resurgent alien invasion force on the moon and kill their alien empress, kill Duke Nukem, and take over the world when both are gone.
Duke encounters them many times during the earlier portions of the DLC, and there are two types of them. The first is a rather plain grey cyborg adorned with Duke's personal symbol, the Nuke Logo, on its chest and eyes. This type is slow moving but wields many powerful EDF weaponry, like the railgun or RPG. The second type is an agile bio-mechanical android that possibly uses cloned genetic material from Duke Nukem himself, as they resemble Duke and are known to spout flesh and blood when destroyed, but their spine and skeletal system are all mechanical. Though Dr. Proton calls these androids "perfect", they possess nowhere near the exact strength and intelligence levels shown by the original Duke Nukem.
Eventually the entire Dukeinator army is destroyed and their creator Dr. Proton being killed by Duke Nukem himself, with any remaining Dukeinators being obliterated by the aliens when a tunnel network of Area 51 was destroyed.
- The Dukeinator was originally going to appear in Duke Nukem Forever as the Human Robot as shown in the 2001 E3 trailer, but was later scrapped.
- After Duke Nukem: Manhattan Project (Mech Morphix's robot), Duke Nukem: Zero Hour (Duke Clones); the Dukeinators (Flesh version only) mark the third time in the Duke Nukem franchise an enemy was designed to look like Duke Nukem.
- When Duke Nukem says "I've got balls of steel" during a voice module verification check for the Duke clones involving Duke's famous one liners; one of the Dukeinators guarding a door corrects him and asks a confused Duke to say "I've got balls balls balls balls of Steel" in reference to the Duke Nukem Ventrilo Harassment video.
- In the final level of The Doctor Who Cloned Me (Duke side of the moon); some dead Dukeninators can be seen throughout the level which reveals that some of them were successful in getting to the moon in an attempt to kill the Alien Empress.