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| Enemy | Appearance | Description |
|---|---|---|
| Assault Trooper | ... | Make use of a jet pack. |
| Assault Captain | ... | Like their 3D counterparts, they have the ability to teleport. |
| Pig Cop | Humanoid Warthog | |
| Alien Ship | ||
| Alien Fighter |
||
| Enforcer | Lizard | |
| Octobrain | Octopus with a big head and three eyes | Able to fire energy blasts, and can use telekinesis to pick up objects and throw them. |
| Baby Octobrain | small infant versions of the Octabrain, they crawl on the ground, unlike the full grown versions and will swarm towards duke. They are known to burst out of imprisoned women, such as those in The Hive level. | |
| Pregnator | Resembles a penis and balls on spider-like legs | Attack by attaching to your face, which will require a quick time event. They will also hurl blobs of goo for a ranged attack. They hatch from oval-shaped eggs. |
| Rat | normal Rat | Rats are not a real threat, except if Duke gets shrunk. |
| Assault Commander | Fat blob on a flying disc | |
| Area 51 Robot (DLC) |
Skeleton-like robot | |
| Duke Clones (DLC) |
Duke Nukem fascimiles | Robotic Clones of Duke created by Dr. Proton. Speak in a robotic voice. |
| Sphere robots (DLC) |
Hovering sphere shaped robots |