Shadow Dancer: The Secret of Shinobi takes place in A.D. 1997, New York City, where Shinobi must face a new threat from a massive reptilian monster that has been terrorizing the city. The ninja master must use his stealth and combat skills to defeat the beast and rescue its hostages.
The gameplay of Shadow Dancer: The Secret of Shinobi is action-packed, with Shinobi navigating through five missions containing three stages each. In contrast to other versions, such as for home computers, this Sega Genesis/Mega Drive exclusive features unique stages and enemy designs. Players must fight against bosses at the end of each mission, and participate in bonus stages where they must shoot flying ninjas.