By approaching enemies undetected, the player character is able to execute a one-hit kill. Additionally, many of the players actions (like running, breaking objects, etc.) will create noise the guards will hear and respond to.

The environments feature sources of light that will reveal the player to any guards nearby. The game features a similar art style to Klei's prior Shank games. However, the tattoos are said to drive anyone received them insane and so the clan's tradition is that any who receive the tattoos must commit suicide after the threat to the clan has been dealt with. He is chosen to receive a series of tattoos that will heighten his senses and make him more agile. After dispatching the attackers, he is instructed to eliminate the head of Hessian Services, a private military corporation responsible for the attack. The game begins with a unnamed ninja in a modern day setting waking up to his clan being attacked. In the tradition of stealth games, emphasis is placed on remaining unseen and unheard. Mark of the Ninja is an side-scrolling stealth action game.

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