The Sega Saturn version of Duke Nukem 3D was a port that was published by Sega and developed by Lobotomy Software. It was released in 1997. It used Lobotomy Software's own game engine, SlaveDriver, instead of the Build engine. The most prominent feature was the dynamic lighting.
- The soundtrack is a limited a group of tracks from Duke Nukem 3D: Atomic Edition, many of which have been remixed/remastered for the Sega Saturn. The levels have different music tracks assigned to them, and the level Urea 51 has a new music track.
- Uses Lobotomy Software's "SlaveDriver" engine instead of the Build engine.
- New menu.
- Similar to Duke Nukem 64, the game has a unique tint for colorized sectors, but with much stronger colors.
- Dynamic lighting in the levels and with objects such as weapons firing or explosions.
- Water, slime, and lava have a new featured look with a much larger tile.
- Walls are aligned with slopes.
- While the tiles represent the original ones, some of them are replaced while still keeping a familiar aspect.
- Some of the encounters are different from the levels in the PC version. Almost every encounter involving the Mini Battlelord tend to be replaced with multiple Assault Commanders; the Mini Battlelord does appear sometimes, though nowhere near as much as he did in the PC version.
- The Sega Saturn version also made use of the Netlink, allowing players to play various game modes, such as deathmatch, online, a rare feature for console games at the time.
- Like Duke Nukem 64, levels are not divided into episodes.
- The levels Spin Cycle, Lunatic Fringe, Tier Drops, and Freeway are missing from this version.
The maps were completely redrawn, albeit in a less detailed aspect. They have a reduced amount of walls or sectors, bigger or higher areas were reduced, and certain levels were divided in two parts in order to save on CPU usage. Levels such as Rabid Transit, Dark Side, and Warp Factor don't have trains due to limitations. In Dark Side and Warp Factor, the trains are replaced with teleporters; in the case of Rabid Transit, the player has to walk between the stations.
Due to a low environment in wall alignment (it is most likely that the walls are completely aligned with sectors), secrets may be easily found in strange aspect walls, especially cracks.
The game contains one exclusive level, Urea 51.
L1: Hollywood Holocaust
L2: Red Light District
L3: Death Row
L4: Toxic Dump
L5: Toxic Dump 2
L6: The Abyss
L7: The Abyss 2
L8: Launch Facility (Secret Level)
L11: Warp Factor
L12: Fusion Station
L13: Fusion Station 2
L14: Occupied Territory
L15: Tiberius Station
L16: Lunar Reactor
L17: Dark Side
L18: Dark Side 2
L20: Overlord 2
L21: Raw Meat
L22: Bank Roll
L23: Flood Zone
L24: L.A Rumble
L25: Movie Set
L26: Rabid Transit
L28: Urea 51 (Secret level)
L29: Hotel Hell