Duke Nukem: Manhattan Project features nine weapons. Six are standard Duke arsenal ones, one shares a similarity and the other two are exclusive. All of them can be carried simultaneously with full ammo and no drawbacks. There are only three types of ammunition in this game - bullets (ammo), G.L.O.P.P. and Pipe Bombs.
Mighty Boot Edit
Duke's preferred (and iconic) melee attack. Kicking an enemy inflicts significant damage to it, but leaves the player vulnerable to a counter-attack. Killing an enemy by kicking it or landing on it will double the EGO boost that death provides. It is also used for sliding kicks, and for crushing de-mutated creatures. When using the Double Damage power-up, most enemies can be gibbed (rendered to bloody pieces) in one kick.
Golden Eagle Pistol Edit
The weapon the player starts the game with. It does less damage per shot than the Mighty Boot, but it can hit enemies at a distance. This pistol (or a similar Desert Eagle design) has since become Duke's signature weapon (silver or gold) and one of his recognizable symbols, despite the Duke Nukem 3D pistol being dark grey and resembling a Glock 17.
A more powerful gun. Good for taking out Pig Cops (especially lower level ones).
Assault Rifle Edit
Has a high fire rate, and overall is about as damaging as the shotgun. This is the weapon of choice for many players, however keep an eye on your ammo level, as the rifle drains it quickly.
A grenade-like explosive, straight from Duke Nukem 3D. It has its own special button for throwing quick pipebombs without having to change weapons. Very useful for blowing things up or taking out enemies from above.
G.L.O.P.P. Ray Edit
A weapon which fires a beam of energy that serves as an antidote to G.L.O.P.P., restoring mutated enemies back to their original forms. Once they are regular creatures again, they can be crushed underfoot. Uses G.L.O.P.P. as ammo. Compare to the Shrink Ray.
Pneumatic Rocket-Propelled Grenade Launcher (PRPG) Edit
The PRPG fires explosive rockets. Uses pipebombs as ammo. Has a much more standard, cylindrical shape compared to the RPG in Duke Nukem 3D.
Pulse Cannon Edit
An oddly shaped weapon which fires bolts of electricity, and can be charged to fire a very destructive ball of lightning. Uses G.L.O.P.P. as ammo.
The secret weapon, unlockable by collecting all Nukes in Hard difficulty. It's a gun which fires lightning and automatically targets all enemies on screen, virtually making you an unstoppable killing machine. Thunder rumbles in the background just when you're holding it, so you know it's a big deal. Furthermore, holding down the attack button when a level loads causes the X-3000 to kill every enemy on the level. Damn, it's good.