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 of time, after which enemies will return to their original patrol routes and one-hit kills on them will once more be possible. Although fighting hand-to-hand with the goal of quickly disabling an enemy is possible, doing so risks being killed or disabled in turn, as well as alerting nearby enemies with a noisy scuffle. Enemies respond to their environment and one another; they will sound an alarm if they unambiguously spot the player character or find a body, which will alert all enemies in the area and prevent them from returning to their previous patrol routes. 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 until they are convinced he is not actually present. They are also subject to terror tactics, and the player can learn to kill and display enemies in a terrifying manner, such as leaving a strangled enemy dangling from a perch or throwing a dead body at an unsuspecting live enemy, causing them to display an exclamation mark over their head, scream, stumble, and fire wildly at anything which scares or startles them.
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. This score is reduced when an alert is sounded by enemy guards. 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. Players get honor 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 honor in three sections: Techniques (passive upgrades and skills such as new one-hit executions), Distraction Items (such as smoke bombs and firecrackers) and Attack Items (such as caltrops and poison-tipped darts). 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, and must be unlocked by completing a number of seals in the form of optional goals related to the specialty of that costume (for instance, optionally terrorizing enemies in specific ways to unlock a costume which improves the ability to terrorize). Completing the game once unlocks a New Game Plus mode where the enemies behave more intelligently and can kill the player with only a single bullet or hand-to-hand strike, the player's line of sight is limited to a cone aimed in whatever direction the player is facing (preventing players from seeing what is behind, above, or below them unless they turn to look), the player is unable to see the enemy's line of sight and must intuit it from the direction an enemy's face is pointed, and the player can no longer detect the radius at which their actions will be heard by enemies.
Plot
The game's story begins with an attack by a heavily armed force on the dojo of the Hisomu ninja clan. The unnamed ninja protagonist, resting after receiving an extensive irezumi tattoo, is awakened by a female ninja named Ora. Gathering his equipment, the protagonist is able to defeat the attackers and rescue his sensei, Azai, as well as several other members of the clan. Before being rescued by the protagonist, Azai was being blamed by the attackers, who said "you picked the wrong people to steal from". However, Azai simply claimed that the clan has been hidden from the modern world for centuries until now, when "their enemies finally found them". Azai tells him about the power of his tattoo and the legend surrounding it, explaining that the ink comes from a special desert flower and grants greatly sharpened senses and reflexes when absorbed slowly into the body, but will ultimately cause one so tattooed with it to descend into madness. 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. Therefore, to receive the Mark, a ninja swears to commit seppuku once the madness begins to take hold.
After the protagonist receives his second tattoo, he and Ora are tasked to take revenge on the PMCs 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. The protagonist invades Hessian's East Asian regional headquarters and murders Corporal Kelly, the Hessian employee who led the attack on the dojo, and, using a stolen GPS tracking unit, stalks Karajan to his castle in Eastern Europe and slays him. 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. Upon being freed, Dosan explains that the flowers from whose leaves the sumi is produced have died out, and appear to have been dead at least since the last fresh supply of the ink was taken by the Hisomu clan. 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. Finally, he ordered that the last of the sumi ink be used to Mark one final ninja, whose strength would enable the heist and save the clan itself from extinction at Hessian's hands. Dosan uses the remains of the sumi to give the protagonist his final tattoo, shortly before some of Azai's high tech ninja stalkers ambush them and shoot Dosan to death as he and the protagonist attempt to escape.
Having left his equipment behind during the hasty retreat, the protagonist, now obviously hallucinating, uses the almost superhuman reflexes afforded to him by the final Mark to evade death at the hands of both the bandits and the Hisomu stalkers, and travels back to Japan with Ora, who recommends he kill Azai for the dishonor of failing to maintain the traditional Hisomu way. The protagonist uses his almost preternatural abilities to infiltrate past Hisomu-jo's new sophisticated defenses, and confronts Azai in his garden. When Ora arrives and commands the protagonist to slay Azai, Azai claims to be unable to see Ora, and, suggesting that she is a symptom of the protagonist's creeping madness, insists that he satisfy his honor and kill himself before he slips too far beyond reason. Suddenly uncertain, the protagonist is reassured by Ora that Azai is lying to deceive him, and she urges him to murder Azai and purge the dishonorable Hisomu clan who followed him. 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. He finds himself in a courtyard opposite both Ora and Azai, who kneels and places his own sheathed sword on the ground, awaiting the protagonist's choice.
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. If the player chooses to kill Ora, the protagonist disembowels himself with the ritual sword and Ora dissolves into inky nothingness as the Marked ninja sputters his last breath and dies in the courtyard.
