Mark of the Ninja is an side-scrolling stealth action game. In the tradition of stealth games, emphasis is placed on remaining unseen and unheard. The game begins with a unnamed ninja in a modern day setting waking up to his clan being attacked. After dispatching the attackers, he is instructed to eliminate the head of Hessian Services, a private military corporation responsible for the attack. He is chosen to receive a series of tattoos that will heighten his senses and make him more agile. 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.
The game features a similar art style to Klei's prior Shank games. The environments feature sources of light that will reveal the player to any guards nearby. Additionally, many of the players actions (like running, breaking objects, etc.) will create noise the guards will hear and respond to. By approaching enemies undetected, the player character is able to execute a one-hit kill. It's also possible to complete the entire game without killing any enemies, with the exception of two named NPC "boss" characters.
Each level has a number of optional goals. Most stealth actions in the game award points, for things like backstabbing guards silently, moving past them with being detected, distracting them, etc. Additionally, there is a bonus for completing the level without being detected and a larger bonus for completing the level without killing anyone. From this, each level has three different scoring tiers. There are also three hidden scrolls in each level, that tell backstory in an audio log-esque fashion. Also, each level has three optional objectives that are unique to the level. Some include destroying a certain number of lights in a level, another may involve moving between two areas under a certain time. Two of optional objectives belong to one of four specific styles (Silence, Nightmares, Hunter or Might), and completing three of the same type will unlock a Style. The Styles offer both advantages and disadvantages that support a certain type of play. E.g. the Path of Silence allow the player to run silently and carry more distraction items, but they cannot stealth kill enemies.
With three scoring tiers, three scrolls and three optional objectives, the player can earn up to 9 Honor points in each level. Honor points are used between levels to purchase various upgrades and items.