| Achievement | How to unlock
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| Back to Bed With You | Knock out an enemy again that was revived from being knocked out.
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| Cordyceps | Dispatch two enemies at once using a body infected with Toxic Fungus.
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| Couldn't Do That Before | Disable a spotlight using the Dusk Moths.
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| Days Long Past | Complete the new Special Edition level.
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| The Humble Moth | Stun an elite guard with moths then dispatch him.
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| Well, I Think It's Interesting | Read one of the history lesson developer commentaries.
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| What Could Have Been | Complete one of the original Mark of the Ninja levels using the Path of Wisdom.
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| Achievement | How to unlock
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|---|
| Awakened | Save Azai from the mercenaries.
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| Crimson Haiku | Perform five different types of stealth kills successfully in one level.
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| Deadly Shadows | Stealth kill a guard from inside a dumpster.
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| Descendent of Iga | Earn three stars in every level.
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| Escape | Escape from the Stronghold.
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| Fated | Determine your fate.
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| Gallows | Terrify a guard using the result of a hanging stealth kill five times.
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| Ghost | Complete a level without killing any guards and without being detected.
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| Haiku | Find all three scrolls in every level.
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| Hisomu's Heir | Kill one guard.
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| Inner Heaven | Kill a guard from inside the box.
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| Karajan's Fate | Assassinate Karajan.
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| Manipulator | Distract 25 guards using your equipment.
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| Marked | Earn all the upgrades.
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| Masterful | Complete a level without getting detected.
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| Mercy | Complete a level without killing any guards.
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| No One Lives Forever | Stealth kill an elite guard after stunning him.
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| Of The Mind | Complete all of the challenge rooms.
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| Oni | Terrorize 10 guards.
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| Perfection | Earn all the Seals in every level.
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| Snare | Use a dead body to lure another guard and then stealth kill them.
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| Stealth Assassin | Perform 25 successful stealth kills.
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| Tactical Espionage Action | Within a single Focus, aim and throw three different types of items.
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| The Dark Project | Get the Undetected honor bonus 10 times in one level.
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| The Mercenary | Assassinate Kelly, the mercenary captain.
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| The Worst Allies | Kill a guard by getting other guards to shoot them.
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| Things Better Left Unseen | Throw the body of one guard to terrorize another.
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| Trickster | Distract 25 guards using environmental objects.
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| True Ninja | Complete the game in New Game Plus.
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| Unstable Footing | Terrify a guard and cause him to stumble to his death.
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