Duke Nukem 3D has four episodes, each divided into several levels. The episodes can be played in any order, although the levels within each episode can only be played in a predetermined order. The original release has three episodes; the Atomic Edition added a fourth, The Birth.
There are several items utilized in levels to aid or hinder player movement.
- Security monitors
These scroll through images from security cameras placed around the level. The cameras are visible to the player, but not destructible. Security monitors can show the locations of enemies that haven't been encountered.
Water comes in two varieties- shallow, which can not be swam in, or deep. Shallow water acts like any other ground; deep water can catch the player if falling. Swimming is accomplished by using the jump and duck keys (and ). Duke has limited air, and will drown if underwater for too long. Watch your health- there is no indication that Duke is out of air other than his health decreasing. Scuba tanks allow for extended periods underwater.
- Lava or goo
Some areas have green goo or red lava. These surfaces will hurt Duke if he stands on them or walks through them. Protective boots avoid this.
In some places, there are drop ceilings or other moving walls that can crush you instantly. Care must be taken to time moving through these areas.
Some areas have panels that shoot shrink rays to shrink the player. This is usually done so the player can pass through a tunnel that is too small for Duke. When doing this, move quickly! If you expand while still in the passage, you will die.
- Cracked walls
Sometimes, a wall will have a spiderweb crack on it. These walls can be blown open with an explosive weapon (RPG, pipebomb, or devastator), revealing secrets or other access to passages.
Yellow barrels (C-9) or other explosive items are around, and will explode if shot. Often these are used to kill enemies or gain access through cracked walls.
- Ventilation ducts
These can be broken open with a kick or shot. They often connect passages or rooms. Some ducts have breakable sides; be careful not to shoot what you are standing on, or you may fall out!
Several areas have elevators for ascending between floors in a building.
Many areas have breakable glass, that breaks with a kick or shot. Once broken, you can walk or jump through the opening.
These allow for visibility around corners. If you walk up to one and press open (space), Duke comments on his looks. Be careful using a shrink ray around mirrors, as they bounce the shrink rays. They cannot be broken with a regular shot or kick, but will break if a pipe bomb is tossed at them.
- Toilets, urinals, and spraying water
"Using" a toilet or urinal with give a +10 health boost, but it can only be done occasionally. If successful, Duke comments, "ah, much better". If not, the toilet flushes. If a toilet, urinal, water fountain, or fire hydrant is broken, the resulting water spray can be drank from by holding open (space) while standing near the water. Unbroken water fountains can be drank from by holding open.
Many areas use red forcefields to restrict access. Walking into an active forcefield will cause injury. While bullets do not travel through them, if one is hit with an explosion, the resulting blast can kill enemies on the other side.
Most doors open with the open button. Some doors are locked and must be opened through other means.
- Fire extinguishers
The can't be used to put out fires. They will, however, explode if shot.
Outlets are located near the floor. The player can duck and press open at these, which causes a shock and takes health away.
Many areas have switchable lights, using light switches on walls. Some lights can also be broken, darkening the room.
Many times, switches are used to control access. Switches come in many varieties, most being two-position. A green light on many means unlocked, while red means locked. Flat button switches can be shot; this is difficult with weapons other than the pistol as they have a tendency to hit the switch multiple times with one burst. Another type of switch is the four-position combination switch, which cycles through four positions. Some areas use a row of switches as a combination lock- the correct combination must be activated to unlock what they control.
At times, you will see women, either bound by aliens, or standing freely. Do not kill these women, or additional enemies will spawn.
- End of level
The end of most levels is a large button resembling a nuclear symbol. When open is pressed, Duke's fist reaches out to push the button. Occasionally, levels end simply by walking into an area. Secret levels are reached through a green level-end button.
Yellow, red, and blue keycards exist to unlock doors. These keycards can be found in the level, and are inserted into a slot by the doors requiring them. This is the typical structure of Duke Nukem 3D levels- find the first keycard to open a door; in the next area, you will find the next keycard for the next door.
The game uses four skill levels, which you choose at new-game. These are:
- Piece of cake (easy)
- Let's rock (normal)
- Come get some (hard)
- Damn I'm good (very hard)
These affect the number of enemies and amount of items spawned. On "Damn I'm good", two additional things happen- cheat codes will not work, and enemies will come back to life after being killed.
There are no "points" awarded in the game. Each level has statistics reported at the end; these are:
- Time taken, as compared to benchmarks "par time" and "3D Realms best time".
- Secrets (total and found)
- Babes saved (Nintendo 64 only)
- Enemies (total and killed; total varies depending upon skill level; highest skill level counts those initially spawned as total, and the player can kill more than the total by killing those that respawn more than once.)