Mark of the Ninja consists of stealth oriented 2D platforming. The character is required to sneak through a series of environments while staying out of sight of guards and performing silent takedowns. Levels are divided into areas of light and darkness; the player character is invisible while in the latter. Sounds such as running may also give away the player character's location and are represented visually by a rapidly expanding circle.unusual for a platformer, Mark of the Ninja employs a line of sight mechanic, meaning that enemies which would be invisible to the character are also invisible to the player, though their sounds are represented on screen in the same manner as the player character's.
By approaching enemies undetected, the player character is able to execute a one-hit kill. To facilitate this, the player can extinguish light sources, hide behind objects and pass through narrow grates and shafts inaccessible to enemies. If detected, they must evade their enemies and remain out of sight for a set period, after which enemies will return to their original positions and one-hit executions will once more be possible. Enemies respond to their environment and one another; they will sound an alarm if they spot the player character or find a body, which will alert all enemies in the area. If they hear a sound or get a glimpse of the player character they become suspicious, displaying a question mark over their head and actively searching for the player character.
The player receives points for executing silent kills, passing by enemies without being detected and achieving optional goals such as recovering artifacts and a series of haiku which tell the history of the ninja clan. This score is reduced when an alert is sounded by enemy guards. Depending on the player's performance on the stages, they earn seals that are used to buy or upgrade skills and weapons and also alternate costumes. Players can get these seals by reaching a specific score on each stage, collecting the secret scrolls, and completing the special objectives present in each stage. Some of the scrolls are obtained through secret challenges, where the player is transported to a room to solve a puzzle.
Before each mission the player is taken to an upgrade screen, where they can spend their seals in three sections: Techniques (passive skills and more types of stealth kills), Distraction Items (such as smoke bombs and firecrackers) and Attack Items (such as spike mines and caltrops). The next screen allows the player to select any unlocked costumes and equip items. Each costume (except the starting one) gives special bonuses, but also a side effect in order to balance its power. Completing the game once unlocks a New Game Plus mode where the enemy AI is smarter, the line of sight is more limited and sounds produce no expanding circles (aside from enemies' footsteps).
