| 21 Decisions, Part 2: Trust
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| 22 Decisions, Part 3: Taking a Stand
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| 23 Public Relations
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| 26 Lockdown
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| 27 Flight Plans
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| 28 Castles in the Air
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| 29 The Fundamental Force
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| 30 Uh-Oh!
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| 33 Ogres in the Shadows
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| 34 Making Your Mark
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| 37 The Bug Bites Back!
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| 38 Targeted for Death!
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| 41 Tug of War!
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| 42 Two Ships
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| 43 Chasing Your Own Tail!
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| 44 Keeping an Ion the Crowd!
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| 45 Heroic Tendencies, Part 1: The Inside Job
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| 46 Heroic Tendencies, Part 2: Heart and Soul
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| 47 Heroic Tendencies, Part 3: Big Problems!
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| 48 Revelations!, The Beginning of the End...
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| 49 Explanations!: The End of the Beginning ...
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| 50 Redemption?
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| 54 Cat & Mouse
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| 55 Humus Sapien!?
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| 56 Beyond Redemption
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| 57 Storm Clouds Gathering
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| 61 Heroes Return, Part 2: Living in a Vise
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| 62 Heroes Return, Part 3: What Would the Mirror Say?
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| 63 Criminal Intent
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| 65 Becoming Heroes, 1: Moving Targets
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| 67 Becoming Heroes, 2: Trust in Fear
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| 69 Becoming Heroes, 3: Green With Envy
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| 71 Becoming Heroes, 4: For the Common Good
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| 74 Becoming Villains, 5: No Win
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| 75 Didn't See That Coming
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| C1 New York's...Finest?
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| C2 Communication Issues
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| C3 Monkey Business
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| C4 Your Mind Knows What It Really Wants
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| C5 Back on Target
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| INT C1 Thunderbolts: Back on Target
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