- "Zilla sends his regards."
- —Evil Ninja at the start of Shadow Warrior Classic.
Evil Ninjas are the most common enemy type in the game and serve as the primary foot soldier for Zilla. They come in five different variations:
Red - Will do everything his brown cousin does, plus he can shoot small rockets at you, as well as shoot Uzis. This variant doesn't use shurikens, but it may drop rockets upon death.
Shadow - The most fearsome of the lot, this ninja uses the ancient skills to stay nearly invisible. He can blast you with two type of magic napalm, one being a wall of fire. Beware, because this ninja is also skilled in use of the flash bomb. Once blinded, you will have little chance of survival. Fortunately, they may drop a flash bomb when killed.
Orange - These ninjas have added ability to shoot heat seeking rockets at you. Very nasty in open areas. After death, they sometimes drop a heat seeking card.
Gray - These ninjas have been upgraded with the ability to launch grenades at you. Considering the blast radius of grenades, these guys are particularly nasty. After death, they can drop grenades.
Mercenaries - Also known as Tong Hitmen, they appear in Wanton Destruction expansion. Act exactly like Evil Ninjas counterparts, except have different visual design. The color of their hats reveal what kind of variation mercenary is.
Evil Ninjas have muscular body. They only wear pants which differ in color depending on ninja type. Their hair are tied in a ponytail. They eyes glow bright red and mouth is full of pointy teeth. Shadow variant is exactly the same except is entirely in black. Mercenary variation has entirely different design, wearing black tuxedo, with sunglasses and a brown hat. Another unique design part is their mustaches.
- Brown Ninjas are the easiest to deal with; they can be chopped up in one katana strike and their shurikens deal little damage; however, they can be quite dangerous in numbers.
- Orange and Red ones are more dangerous because of their ability to shoot rockets, the latter firing homing missiles. When fighting them, it is best to keep enough distance to have time to dodge when they shoot their rockets at you. The same goes for Gray Ninjas. The danger in these enemies is the immense and immediate damage they'll deal to you if they fire explosives up close; always keep your distance. Keep in mind that they can withstand a few katana slashes before being dismembered.
- Shadow Ninjas are the most dangerous of the bunch. They can easily blend in with their surroundings and be hard to see even when not running wildly about. He shoots two variants of the Guardian's Head fireballs: one fireball which shoots smaller shots as it goes, and one consecutive wall of fire straight forward. The Shadow Ninja is especially lethal thanks to his restraint from shooting his Uzi at you, "revealing" himself only to fire this second variant of fireball, which deals deadly amounts of damage. Terminate with extreme prejudice; a good way to soften them up is to disengage and throw a Gas Grenade or sticky bomb at their location, then returning after damage has been dealt.
- Though they are called "Ninjas" in the game, aesthetically they look nothing like ninjas or anything even resembling a human.
- Evil Ninja is the only regular enemy that can be heard speaking in Shadow Warrior Classic.