When private military forces attack the Hisomnu ninja clan, an unnamed Ninja who's in a deep slumber is awoken. He defends his clan, aided by a female ninja named Ora. Later, he learns that he is marked by a legendary Irezumi tattoo, capable of making him extremely agile and deadly.

The Ninja sets out to claim revenge and find out the reason for the attack. With every mission, he receives another mark that strengthens him, but he soon learns that the ultimate end of this super power is death. Mark of the Ninja combines acrobatics with strong stealth elements, where players must infiltrate the enemy stronghold and assassinate those responsible for the massacre at the Hisomnu dojo.