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Duke Nukem 64 doesn't have any episodes, instead the player has to do all the levels to progress. Most of the original level's are present except for the hidden levels Spin Cycle and Tier Drops, which were replaced by two levels from the Atomic Edition, namely Duke Burger and Area 51.
In addition many of the levels were modified to included new areas. Also, the level numbers have been changed slightly - Hollywood Holocaust is listed by the game as level 0.
Level 0: Hollywood Holocaust: There is now a store, which is locked from the outside but can be accessed via a secret teleporter hidden in the wall to the right of the auto destruct button.
Level 1: Red Light District has been renamed 'Gun Crazy' - the bookstore is now a gun shop and the whole strip bar area has been changed to a Duke Burger resturant. The strip club is now an outdoor area with boxes. Also, the modified RABID TRANSIT can also be glimpsed at the top left just as you come out of the lift at the very start of the level. The first secret level 'Duke Burger' can be accessed from this level.
Level 2: Death Row: The chapel has been replaced by a cellblock featuring Hannibal Lector due to Nintendo not allowing religious references. The secret behind the bed has been expanded and leads to the mangled corpse of Snake Plissken (Kurt Russell's character from ' Escape From New York and Escape From LA)', which prompts Duke to say 'I guess he didn't escape from L.A!' (this secret also appears on the Atomic Edition level 'Shop-N-Bag')
Level 3: Toxic Dump: This level remains unchanged.
Level 4: Launch Facility : This level is now a regular level.
Level 6: Battlelord The first encounter with the Battlelord is now a separate level.
Level 7: Duke Burger (Secret level) One of two levels from the Atomic edition to make an appearance. A shipping facility is added to the start and references to dog meat are replaced with hung pigs.
Level 8: Spaceport: This level remains unchanged.
Level 9: Incubator: This level remains unchanged.
Level 10: Warp Factor: This level remains unchanged.
Level 11: Fusion Station: This level remains unchanged.
Level 12: Occupied Territory: This level remains unchanged, but there is no secret exit as Spin Cycle has been dropped from the N64 version, possibly due to the limited capacity of Nintendo 64 cartridges.
Level 13: Tiberius Station: This level remains unchanged.
Level 14: Lunar Reactor: The hanging corpse of Luke Skywalker has been replaced with a corpse of Yoda.
Level 15: Dark Side - The level is now significantly shorter. There is no gamma transport. the outer area near the beginning has been deleted. some portions are still present, like the room over rooms, but are unaccessible without a cheat device. The blue Access Card room from Duke Nukem 3D is now a secret area.
Level 17: Overlord: See above.
Level 18: Lunatic Fringe (secret level): This level remains unchanged.
Level 19: Raw Meat: The stage area with the dancing woman now has cage around it and inside are the 'Duke Brothers'
Level 20: Bank Roll: The area with the revolving walls has been replaced with a long red corridor which leads to a small room which, depending on difficulty, features lots of annoying Turrets which in turn leads to another room with a big pool in the middle.
Level 21: Flood Zone: There is a whole new building in which you must swim up to the top floor to find the yellow access card. Also the rooftop with the red access card door now features a helipad and control room.
Level 22: L.A. Rumble: There is a secret dungeon where the Doomguy can now be found. Also, a UFO can be seen behind the helicopter destroying a building.
Level 23: Movie Set: The level has been extended and includes a new set for a movie based around Area 51. The red panel opens up a secret area which leads to a hidden exit to the level Area 51. The exit to 'TIER DROPS' has been removed as that level was dropped from this version.
Level 24: Rabid Transit: Has been significantly modified: The platform you use the blue access card to open has been moved to a new area to the right of when you enter the start of the level (opposite the book stand), where there is a motionless train and a lost and found office. The train from the main platform only goes in one direction to another new area (where a look-alike of L2: GUN CRAZY (formerly: RED LIGHT DISTRICT) can be seen) in which you have blow open the crack in the wall which leads to a car park where the Blue access card can be found.
Level 25: Fahrenheit: The fire station now has an office, kitchen and crew quarters. (There is also a new secret room in one of the windows on the far end wall)
Level 27: Stadium: Now has a roof and, during Duke matches, the player can explore the changing rooms and offices underneath the stands.
Level 28: Area 51 (secret level) The second and final level from the Atomic edition to make an appearance here. This level remains unchanged, although the start has been moved to the long dark tunnel that leads to the entrance which needs the Blue key. The starting area from the Atomic Edition may possibly still exist.
Level 29: Freeway: Now has a police station to explore. Mini Overlord makes another appearance here.
Piracy: A shortened version of the level 'Babe Land' from the 'Atomic Edition expansion pack. Some portions of the level still exist, like the hidden vent which leads back to the fountain found in Duke Nukem 3D Atomic Edition, but some have changed completely. The location of the exit button in this map has been placed near the castle.
Castle Dukenstein: A dark level revolving around a haunted mansion. The level's name is a reference to id Realm's Wolfenstein. Thunder sounds constantly play around the map, possibly adding music to the level. It may possibly have been a regular level.
Noctis Labyrinthus: A super-secret multiplayer map based off the Noctis Labyrinthus labyrinth on Mars. Lots of obstacles like cliffs and pits are present. Can be accessed with the level select cheat or activating the four secret switches in Shaft.