A remastered version was released on October 9, 2018, for Xbox One, PlayStation 4, Nintendo Switch, Microsoft Windows, macOS, and Linux by Klei Entertainment.

[5] The player receives points for executing a variety of tactics such as silent kills, passing by enemies without being detected, successfully preventing the discovery of bodies, terrorizing opponents to cause them to fall into disarray, and achieving optional goals such as recovering artifacts and a series of haiku which tell the history of the ninja clan.

Depending on the player's performance on the stages, they earn honor and complete seals that are used to buy or upgrade skills and weapons and also unlock alternate costumes.

In the distant past, the first Hisomu ninja to receive the Mark became incredibly dangerous, but increasingly deranged, leading to a lengthy reign of terror that only ended with his demise.

After the protagonist receives his second tattoo, he and Ora are tasked to take revenge on the PMC responsible for the attack on the dojo: a corporation called Hessian, run by a ruthless Eastern European plutocrat named Count Karajan.

Meanwhile, the horishi artist Dosan expresses concern over the tattoo ink's quality and promises to learn why Azai has not procured a fresh supply.

Upon returning home, the protagonist and Ora see that their clan has stolen a great deal of high tech military equipment from Hessian, leaving them to realize that Azai's plan had been to rob Karajan and replace the old Hisomu Path with a modern, technological approach to espionage.

Instead of committing seppuku, the protagonist flees with Ora to find Dosan, who had left a message indicating that he had personally gone in search of the mysterious desert flower.

Following his trail, the protagonist and Ora discover that Dosan has been captured by bandits, who are holding him hostage in a war-wracked Middle Eastern city and demanding that he Mark them with his remaining supply of the sumi ink.

As revealed by hidden scrolls recounting the history of the clan, Azai himself had failed to defend the flowers when the devastated region to which they were endemic was taken over by vicious bandits.

Thus dishonored, but for the sake of the clan's survival, Azai hid his failure and had planned the Hessian heist in order to supply the Hisomu with cutting-edge equipment now that the unique source of their strength had been extinguished.

Upon retrieving the ritual sword, the protagonist experiences a brief psychotic fugue state, in which he symbolically relives the events of his life subsequent to taking on the Mark.

If the player chooses to kill Azai another psychotic episode follows, in which the protagonist murders his sensei and becomes the maniacal Hisomu tyrant of legend, melting silently into darkness with a swift strike of his sword.

Following Klei's announcement on February 28, 2012, that it was developing Mark of the Ninja, the game featured at the Penny Arcade Expo East in Boston, Massachusetts in April 2012.

[29] Garrett Martin of the Boston Herald give high marks for the game's cutscenes and stated they were "good enough to warrant a Cartoon Network TV show.

[16] Official Xbox Magazine's Andrew Hayward also gave high marks for the visual atmosphere of the game, and further praised the "wealth of options" to complete missions.

Kotaku's Patricia Hernandez felt that the game had too many puzzles involving laser traps, and noticed that guards would on rare occasion "glitch out and not move and just look back and forth, making stealth impossible.

Awards, the Academy of Interactive Arts & Sciences nominated Mark of the Ninja for "Downloadable Game of the Year" and "Outstanding Achievement in Animation".