| Trophy | How to unlock
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| - 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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| - 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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| - Perform five different types of stealth kills in one level.
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| - 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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| - Terrify a guard with a hanging stealth kill five times.
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| - Complete a level without killing any guards and without being detected.
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| - Find all three scrolls in every level.
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| - Kill a guard from inside the box.
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| - Distract 25 guards using your equipment.
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| - Earn all of the upgrades.
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| - Complete a level without getting detected.
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| - 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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| - Complete all of the challenge rooms.
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| - Earn all three seals in every level.
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| - 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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| - Stun an elite guard with moths then dispatch him.
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| - 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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| - Distract 25 guards using environmental objects.
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| - 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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