Proton, the villain of Duke Nukem, was originally intended to be the enemy in this game, but was replaced by Mech Morphix to avoid possible continuity problems with Duke Nukem Forever, in which Dr. The game shares many similarities with the original Duke Nukem game, such as they are both side-scrollers, and both games have a half-robotic mad scientist as the main enemy. It is not a direct sequel to any game, and is instead a stand-alone spin-off game however, each earlier game in the series featured a completely different story and a new enemy force for Duke to mess up as well, with only the second and third games directly connected chronologically. This allows the path the player takes through the levels to bend and twist somewhat, although the paths are still fixed. The game is a side-scroller, but it is set in a 3D environment. Levels in the game contain recognizable parts of New York City. There are also a number of enemies that have not been mutated from anything, such as the FemMech, a sadistic and agile feminine robot that wields a lethal whip. These creatures include alligators, rats, cockroaches and boars. (Gluon Liquid Omega-Phased Plasma) to mutate creatures into deadly monsters, which are then taking over Manhattan Island, New York City.

This time fighting the evil mad scientist Mech Morphix who is using a radioactive slime called G.L.O.P.P. Manhattan Project features the humorously chauvinistic action hero Duke Nukem who must save the day once again.

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