| Trophy | How to unlock | Type
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| - Combo Boxing Glove into Bees.
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- A Consummate Professional
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| - Recruit five Henchmen in a single game.
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| - As Max, create twenty Golden Statues, and add them to the Inner Sanctum.
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| - Recruit 300 minions at once.
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- Assuming Indirect Control
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| - Knock a Frozen Agent into a Shark Tank.
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| - Bounce one Agent against three Pinball Bumpers.
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| - Fire V.O.I.D. for the first time.
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| - Fire H.A.V.O.C. for the first time.
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| - Knock a Frozen Agent into a Pinball Bumper.
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| - Complete a Campaign on Easy difficulty.
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| - Combo Giant Fan into Flamethrower.
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| - Set H.A.M.M.E.R.'s Super Agent aflame.
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- Float like a Butterfly...
| - Combo Giant Fan into Boxing Glove.
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- Fulfilling Your Expectations
| - Defeat every Super Agent once and for all.
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- Get The Gang Back Together
| - As Ivan, recruit some old friends.
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| - Execute a loyal Henchman.
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| - As Emma, complete all the Genius Upgrade Research.
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- I'll Take Care of This Myself
| - Defeat a Super Agent with your Genius.
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| - Fire V.E.N.O.M. for the first time.
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| - Combo Giant Fan into Laser Wall into Shark Tank.
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| - Combo Giant Fan into Shark Tank.
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| - As Emma, capture and mock a pale imitation during 'The Melting Point Of Steele.'
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| - As Ivan, kill fifty Agents using an old school weapon.
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| - Have one million Gold in the Vault.
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- Perfectly Balanced, As All Things Should Be
| - Allow the finest Rogue in the world to succeed.
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| - As Zalika, research everything.
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| - Drop a certain agent into a specific trap.
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| - As Max, have 200 Specialist minions in the Lair at once.
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| - Combo Bubble Cannon and Slippery Floor.
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| - As Zalika, steal an extinct creature, one that is yet to hatch, and a treasure from another world.
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- The Man With the M.I.D.A.S. Touch
| - Fire the M.I.D.A.S. Device for the first time.
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| - Complete a Campaign on Normal difficulty.
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| - Have one Region enter Lockdown.
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| - Defeat the finest Saboteur in the world with Jubei.
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| - Destroy every Region. Permanently.
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| - Take care of an intruder, and then destroy the evidence.
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| - Blow a Gas Cloud into an Agent with a Giant Fan.
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| - Complete a Campaign on Hard difficulty.
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| - Steal every available Loot item in a single playthrough.
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