Doctor Morbis is back with a new subhuman! He wants to stop the Cheetamen from ruining his evil plans! He creates the Ape Man. The strongest subhuman yet! Doctor Morbis plans to use the Ape Man to destroy his failed experiment... Aries! Apollo! And Hercules! You must help the Cheetahmen fight Doctor Morbis and his evil team of mutants.
In Cheetahmen II the player assumes the role of one of the three Cheetahmen (Aries, Apollo and Hercules), and upon defeating an enemy boss at the end of the second level, they switch to the next Cheetahman for the following two levels as in the Action 52 version. However, the order that they appear is reversed in this game, with Apollo being used in the first two levels.