| Trophy | How to unlock
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| A Perfect Algorithm (Bronze) | Complete "The Warder of the Brain" with a perfect score in every battle.
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| A Perfect Assassin (Bronze) | Complete "Death Will Have His Day" with a perfect score in every battle.
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| A Perfect Congress (Bronze) | Complete "Once More Unto the Breach, Dear Friends" with a perfect score in every battle.
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| A Perfect Cousin (Bronze) | Complete "Of His Bones Are Coral Made" with a perfect score in every battle.
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| A Perfect Detective (Bronze) | Complete "Foul Deeds Will Rise" with a perfect score in every battle.
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| A Perfect Diplomat (Bronze) | Complete "The Head that Wears a Crown" with a perfect score in every battle.
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| A Perfect Disposal (Bronze) | Complete "The Isle Is Full of Noises" with a perfect score in every battle.
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| A Perfect Economy (Bronze) | Complete "He That Dies Pays All Debts" with a perfect score in every battle.
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| A Perfect Escape (Bronze) | Complete "The Tempest" with a perfect score in every battle.
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| A Perfect Friend (Bronze) | Complete "To Revenge is No Valour" with a perfect score in every battle.
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| A Perfect Intelligence (Bronze) | Complete "All that Lives Must Die" with a perfect score in every battle.
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| A Perfect Investment (Bronze) | Complete "If Money Go Before, All Ways Do Lie Open" with a perfect score in every battle.
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| A Perfect Librarian (Bronze) | Complete "In Nature's Infinite Book of Secrecy" with a perfect score in every battle.
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| A Perfect Patriot (Bronze) | Complete "The Evil That Men Do" with a perfect score in every battle.
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| A Perfect Pursuit (Bronze) | Complete "They Stumble that Run Fast" with a perfect score in every battle.
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| A Perfect Rebellion (Bronze) | Complete "The Rude Eye of Rebellion" with a perfect score in every battle.
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| A Perfect Rescue (Bronze) | Complete "Yet Death Will Seize the Doctor" with a perfect score in every battle.
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| A Perfect Retrieval (Bronze) | Complete "The Arms Are Fair" with a perfect score in every battle.
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| A Perfect Sabotage (Bronze) | Complete "When Beggars Die, There Are No Comets Seen" with a perfect score in every battle.
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| A Perfect Salvage (Bronze) | Complete "For One to Say a Soldier Lies" with a perfect score in every battle.
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| A Perfect Soldier (Bronze) | Complete "Journeys End in Lovers Meeting" with a perfect score in every battle.
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| A Perfect Son (Bronze) | Complete "What Thing Had My Father Lost" with a perfect score in every battle.
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| A Perfect Trial (Bronze) | Complete "A High Hope for a Low Heaven" with a perfect score in every battle.
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| A Perfect Warrior (Bronze) | Complete "To Follow Mine Own Teaching" with a perfect score in every battle.
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| AMPed Up (Bronze) | Deal a total of 300 damage using Damage();.
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| Boom Shaka-Laka (Bronze) | Kill a total of 25 enemies using Grenade.
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| Change of Heart (Bronze) | Change a companion's ideology.
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| Element: Perfection (Gold) | Complete the game with a perfect score in every battle.
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| Facing the Tempest (Bronze) | Defeat the infiltrator.
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| Hack Yeah! (Bronze) | Hack 5 turrets with Hacking Protocol.
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| Hey Arthur! (Bronze) | Square off against Arthur.
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| Inspirational Speaker (Bronze) | Get the Galactic Congress to rule in your favor.
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| Keep Your Allies Close (Bronze) | Gain a faction's loyalty.
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| Lab Safety (Bronze) | Save at least 2 scientists.
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| License to Skill (Bronze) | Max a skill.
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| Looks Like We Made It (Bronze) | Get invited to the Galactic Congress.
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| Man of Action (Bronze) | Stop Il Pugno Rosso and find Emilio.
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| No One's Perfect (Silver) | ...But this ending could be. Achieve a perfect ending.
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| No Pain, No Gain (Bronze) | Damage 5 units at the same time using Share the Pain.
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| On the Brink (Bronze) | Kill an enemy by knocking them off a ledge with Earth Dash.
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| Perfect Space (Platinum) | Obtain all Trophies in Element Space.
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| Power of Persuasion (Bronze) | Stop the assassin from killing the Empress.
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| Roll the Dice (Bronze) | Infiltrate the casino and rendezvous with your informant.
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| Secondary Education (Bronze) | Win all secondary missions across multiple playthroughs.
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| Shutdown (Silver) | Defeat the Hacker by destroying his energy sources.
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| Soul Purpose (Bronze) | Have a Soul Possessed Ally kill an enemy.
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| Survivor (Gold) | Win the game in Extinction Mode.
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| Swap and Kill (Bronze) | Use Quantum Swap and kill the swapped enemy in 1 turn.
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| Top of the Class (Bronze) | Max an archetype.
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| Trial by Combat (Bronze) | Prove yourself to the Prince.
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| True Blue (Bronze) | Gain a companion's loyalty.
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| Unlocked and Loaded (Bronze) | Unlock a tier 2 weapon.
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| Up in Arms (Bronze) | Unlock a tier 3 weapon.
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| Welcome to the Gun Show (Silver) | Unlock all weapons (across multiple playthroughs).
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| Why Tank You! (Bronze) | Blow up a tank.
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| Workaround (Bronze) | Damage a unit with Tank Armor using Trick Shot.
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| Zero's Hero (Bronze) | Regain control of Zero's chassis and your ship.
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