The Cycloid Emperor is the leader of the alien invaders. Encountered on Stadium, it attacks the player with a rapid-spread version of the Octabrain's mental blast at close range. It will also fire a large barrage of missiles at a distance, inflicting the same amount of damage as Duke's RPG.
The Cycloid Emperor has 4500 hit points and is unaffected by the Shrinker. The Cycloid Emperor ranks as one of the most dangerous of the bosses in Duke Nukem 3D due to the erratic nature of its main attack, which fire rockets in salvos of 2-3 per shot. The Cycloid Emperor's other attack, the mental orb spray, is activated only at short to medium range.
When Duke first encounters the Cycloid Emperor, he utters "It's down to you and me, you one-eyed freak!" Upon dying, Duke will say, "Die, you son of a bitch!"
If placed on user maps with the default palette of 0, the Cycloid Emperor will only be able to walk on sectors with a Lotag of 3. This is why it cannot leave the field in Stadium and why it usually cannot move from its initial position.
As with the Overlord and the Alien Queen, the Cycloid Emperor's programming used the Battlelord as a base template, and there is leftover code in the Cycloid Emperor. While in another palette, the Cycloid Emperor has the same appearance as the Battlelord Sentry and only 1 hit point. Also, the rockets launched from the Cycloid Emperor will not spawn correctly and will actually cause it to kill itself if it does not have the correct palette.
If an off-palette Cycloid Emperor is artificially given a smaller size, this self-destruction does not occur.
Some of the Cycloid Emperor's roars are similar to the T-Rex from Jurassic Park.
There is an unused alert sound (b2rec03.voc) that never made it into the game, since Duke is instead heard talking. The sound is used in the Sega Saturn version by the Overlord.
In Duke Nukem: Total Meltdown, the Cycloid Emperor looks similar to the original one found in Duke Nukem 3D in shape and size, but its hue is much darker.
In the Duke Nukem 64 port, the Cycloid Emperor is rendered with polygons and is the only fully 3D enemy in the game. In addition, it is larger, slower, and has more health than in the PC version. It also fires rockets with its left arm instead of its right. Upon reaching one-third of its health, it will replace the rockets it fires with half-charged plasma bolts.
In Duke Nukem: Zero Hour, the final boss, Zero, appears to be a Cycloid himself, being as tall as the Cycloid Emperor and having a similar appearance.