Spoiler
Level extras
Starting locations

Player one starting location is missing the sector bit of information in the maps extracted from the ROM. in Build engine, besides the xyz coordinates, the sprites also have the sector information, which makes it possible to have multiple areas that coexist in the locations, an effect that has been widely used in Lunatic Fringe level.
In Lunatic Fringe, instead of starting near the original location of the PC version, the player start on the very other side of the 720º circle in mid of a bunch of enemies!

Since this is in the very same coordinates as the place you start in the actual game, was the player meant to start here instead?
Skies

The sky textures are not rendered in the actual game. In fact, most of the maps just replaced the skies with some random textures, making it really weird to look at them in a standard editor of Duke 3D. However Castle Dukenstein and Noctis Labyrinthus levels have been created with the skies in mind (which also mean they have been created very easly in development). These textures are interesting to check. Since the sky in Noctis Labyrinthus uses a palette, in the actual game projectiles will hit it as if there was a barrier.
Fog intensity

There has been some work with sector fog intensity in the maps. Despite that the visibility is leveled in the actual game.
Palettes

There is some work with palettes in the levels which cannot be seen in the actual game since most of the palettes have been removed. In the example above from Raw Meat, the microphone is green, the tables are blue and the Karaoke sign is grey.
Of course this may not be necessarily considered leftover content, since in Duke 3D some palettes are also replaced by the palette of the sector. In the example above, the tables would be completely blue regardless of the palette of the sprites themselves.
Level extras
Starting locations

Player one starting location is missing the sector bit of information in the maps extracted from the ROM. in Build engine, besides the xyz coordinates, the sprites also have the sector information, which makes it possible to have multiple areas that coexist in the locations, an effect that has been widely used in Lunatic Fringe level.
In Lunatic Fringe, instead of starting near the original location of the PC version, the player start on the very other side of the 720º circle in mid of a bunch of enemies!

Since this is in the very same coordinates as the place you start in the actual game, was the player meant to start here instead?
Skies

The sky textures are not rendered in the actual game. In fact, most of the maps just replaced the skies with some random textures, making it really weird to look at them in a standard editor of Duke 3D. However Castle Dukenstein and Noctis Labyrinthus levels have been created with the skies in mind (which also mean they have been created very easly in development). These textures are interesting to check. Since the sky in Noctis Labyrinthus uses a palette, in the actual game projectiles will hit it as if there was a barrier.
Fog intensity

There has been some work with sector fog intensity in the maps. Despite that the visibility is leveled in the actual game.
Palettes

There is some work with palettes in the levels which cannot be seen in the actual game since most of the palettes have been removed. In the example above from Raw Meat, the microphone is green, the tables are blue and the Karaoke sign is grey.
Of course this may not be necessarily considered leftover content, since in Duke 3D some palettes are also replaced by the palette of the sector. In the example above, the tables would be completely blue regardless of the palette of the sprites themselves.

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