The player begins the game as Joe Musashi (the Red Ninja), whose mission is to retrieve five elemental crystals that were stolen by the enemy and spread across different locations. Similarly to the original G.G. Shinobi, the first four stages can be played in any order and after defeating the boss of each stage, Musashi will be joined by one of his allies, allowing the player to control them as well.
The game begins with Joe Musashi (the Red Ninja) as the protagonist, tasked with retrieving five elemental crystals stolen by the enemy and placed in different areas. Similar to G.G. Shinobi, the first four stages can be completed in any order after defeating each boss, allowing the player to control one of Musashi's allies.