| 14 Casualties of War!
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| 15 Wanted Dead or Alive
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| 16 Thunder & Lightning
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| 17 Matters of Gravity
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| 20 Decisions, Part 1: Turning Point
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| 21 Decisions, Part 2: Trust
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| 22 Decisions, Part 3: Taking a Stand
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| 24 The Eye of the Storm
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| 26 Lockdown
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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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| 31 A More Perfect Union
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| 32 Blood Sports
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| 33 Ogres in the Shadows
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| 34 Making Your Mark
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| 35 The Inheritance
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| 36 How Is Justice Best Served?
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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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| 48 Revelations!, The Beginning of the End...
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| 54 Cat & Mouse
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| 56 Beyond Redemption
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| 57 Storm Clouds Gathering
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| 58 Degrees of Evil
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| 59 Silent Scream
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| 60 Heroes Return, Part 1: Brave New World?
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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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| 64 City of Hope
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| 66 Becoming Villains, 1: Empyrean Blues
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| 68 Becoming Villains, 2: Trust in Fear
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| 70 Becoming Villains, 3: Souls in the Balance
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| 72 Becoming Villains, 4: Malignant Tumors
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| 74 Becoming Villains, 5: No Win
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| 75 Didn't See That Coming
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| 101 Why Ask Why?
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| 102 Rush
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| 103 Taking Civil Liberties, Part 1
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| 104 Taking Civil Liberties, Part 2
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| 106 Power Hungry
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| 107 Power Full
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| 108 Power Outage
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| 109 Beyond Redemption
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| * AN2 Annual '2000: Under the Surface
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| B7 No Going Back, Part 1: Not What We Planned
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| B8 No Going Back, Part 2: Should I Stay or Should I Go
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| B9 No Going Back, Part 3: Stray Signals
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| B10 Return of the Masters, Part 1: Bonds Unbroken
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| B12 Return of the Masters, Part 3: Broken Toys
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| INT B2 No Going Back
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