The evil Spider has used his time machine to change history, and it is up to the Ninja Commandos to set things straight. Your mission is to infiltrate Spider's base and use his time machine to go into the past. There, you must defeat his soldiers and finally Spider himself in order to fix the corrupted timeline.
There are three commandos to choose from, each with special powers: Joe Tiger, an American descendent of ninjas; Rayar Dragon, a female archery specialist; and Ryu Eagle, a descendent of the Fuma ninjas.
The game is played on a vertically scrolling screen, and each commando can shoot projectile weapons, do somersaults and has a special "ninja trick" that does a devastating amount of damage to your enemies but reduces your life bar by approximately one-fourth.
The arcade coin-op version of Ninja Commando is nearly identical to the Neo Geo home version, due to the fact that they run on the same hardware. The only difference in the home version is that you have a limited amount of continues, whereas the in the arcade version, the number of continues is limited only by your supply of quarters.