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