As with the original games, Shinobi for the GG (the first portable member of the franchise) is a action side-scroller in which you take the role of an elemental ninja seeking revenge, your task to clear several stages filled with evil ninja and other assorted enemies.

New to this release is the MegaMan-like ability to select which stage (all also unique for this release) to play in any sequence. Each stage contains a fellow elemental ninja held prisoner, who gets released once you complete the level. You can then switch between available ninja mid-stage to take advantage of their unique abilities (green ninja double jumps, blue ninja has a grappling hook, yellow ninja walks on water, etc.) which become a necessity to successfully complete all the levels.