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 Starfleet-only
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| Tutorial
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 “Graduation Day” • “Routine Maneuvers” • “Trial by Fire” • “The Shadow Knows” • “Children of War” • “Reporting In”
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 “I Sing of Arms” • “Search and Rescue” • “Bull by the Horns” • “Dislodging Klingons” • “The Taurean Affair” • “Earthward Bound”
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 “Graduation Day” • “Training Cruise” • “Field Promotions” • “Communication Breakdown” • “Assimilation of the Innocent”
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| Agents of Yesterday
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“Explore Earth Spacedock” • “In the Shadow of Cestus” • “Painful Omens” • “Return to Babel” • “Tangled Webs” • “The Battle of Caleb IV”
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| Klingon War
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“Welcome to Earth Spacedock” • “Diplomatic Orders” • “Stranded In Space” • “Researcher Rescue” • “Secret Orders” • “The Doomsday Device” • “The Galaxy at Large”
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| Romulan Mystery
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“Heading Out” • “Empress Sela” • “Desperate Measures” • “Shadow Play” • “Taris”
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| Klingon Defense Force-only
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| Tutorial
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“End of Watch” • “Red Alert!” • “Intruder Alert” • “Challenge for Command” • “Your New Command” • “Journey to Qo'noS”
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| Empire
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“Duties of Command” • “The Hunt is On” • “Space Chase” • “Manhunt” • “Friend or Foe”
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| Warzone
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“Bringing Down the House” • “The House Always Wins” • “Mars, the Bringer of War” • “Alpha”
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| Fek'Ihri Return
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“Blood of the Empire” • “Destiny” • “Afterlife”
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| Romulan Republic-only
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| Tutorial
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“A Day on the Farm” • “A Day in the Sun” • “Virinat, Invaded” • “Flight from Virinat”
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| From the Ashes
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“Explore the Flotilla” • “The Helix” • “Crossroads at Crateris” • “Gasko Blues” • “The Search for New Romulus” • “Turning Point” • “Neutral No More”
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| Allies
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“The Price of Neutrality” • “Memory Lane” • “Bigger Picture” • “Smash and Grab” • “Tradecraft”
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| In Shadows
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“An Inside Job” • “Enemy Action” • “Sleepers” • “Cloak and Dagger” • “Revelation” • “Mind Game”
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| Wasteland
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“Secrets of Nimbus” • “The Lost City of Paradise” • “Blind Men Tell All Tales” • “The Undying” • “A Fistful of Gorn” • “Installation 18”
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| Vengeance
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“Voice of the Voiceless” • “Abducted” • “Small Packages” • “Last Stand” • “The Best Defense” • “Turnabout” • “Devil's Choice”
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| Freedom
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“Toward Freedom”
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| Dominion-only
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| Engineered for War
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“Hunt” • “Ceremony” • “Turn the Tide”
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| Cross-faction
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| Cloaked Intentions
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“The Vault” • “Mine Enemy” • “Frozen” • “Coliseum” • “Cutting the Cord” • “Darkness Before the Dawn”
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| Cardassian Struggle
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“Lost and Found” • “Spoils of War” • “Jabberwocky” • “The Factory” • “The New Link”
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| Borg Advance
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“Task Force Operations” • “Report on Borg Activities” • “Where Angels Fear to Tread” • “A Gathering Darkness” • “Assimilation” • “Fluid Dynamics”
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| New Romulus
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“New Romulus Aid” • “Staging Area” • “Hidden Camera” • “Warehouse” • “Mountain Base” • “Secret Shuttle Codes” • “Overgrown Caves” • “Web Access” • “Latest Findings” • “The Power Source” • “Secrets of the Ancients”
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| Solanae Dyson Sphere
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“Sphere of Influence” • “Circles within Circles” • “Supply Woes” • “The Contested Zone” • “The Omega Standoff” • “Tower Control” • “A Step Between Stars” • “Fluidic Destruction” • “Surface Tension”
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| Delta Quadrant
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“Escalation” • “Mindscape” • “Reunion” • “Friends in Unlikely Places” • “Revelations” • “Enemies in All the Usual Places” • “All That Glitters” • “The Kobali Front” • “Capture the Flag” • “The Dragon's Deceit” • “Alliances” • “Know Your Enemies” • “Revolution” • “Taking Care of Enemies” • “Takedown” • “What's Left Behind” • “Dust to Dust”
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| Iconian War
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“Uneasy Allies” • “Blood of Ancients” • “Delta Flight” • “House Pegh” • “Time in a Bottle” • “Broken Circle” • “Butterfly” • “Midnight”
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| Yesterday's War
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“Temporal Ambassador” • “The Once and Future Agent” • “The Core of the Matter” • “Vorgon Conclusions” • “Terminal Expanse” • “Survivor”
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| Future Proof
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“Sunrise” • “Stormbound” • “Time and Tide” • “The Temporal Front” • “Temporal Reckoning” • “Ragnarok”
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| New Frontiers
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“Echoes of Light” • “Of Signs and Portents” • “Mirrors and Smoke” • “Brushfire” • “Beyond the Nexus” • “Melting Pot” • “Scylla and Charybdis” • “The Renegade's Regret”
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| Gamma Quadrant
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“Storm Clouds Gather” • “Armistice” • “The Search” • “Doomed to Repeat” • “Quark's Lucky Seven” • “Tenebris Torquent” • “Home”
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| Age of Discovery
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“The Plausibility of the Possible” • “Impossibility of Reason” • “Secrets” • “Downfall”
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| J'Ula's Discovery
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“Para Pacem” • “Illusion of Communication” • “Beneath the Skin” • “Sentinels” • “Rescue and Search” • “Within The Briars” • “The Ninth Rule” • “Ruins of Doom” • “The Measure of Morality (Part 1)” • “The Measure of Morality (Part 2)”
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| Klingon Civil War
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“The Centre Cannot Hold” • “The Khitomer Discord” • “Partisans” • “Knowledge is Power” • “Leap of Faith”
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| Some missions may appear in alternative orders for some factions.
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| Side Content: The Galaxy at Large
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| Spectres
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“Spectres” • “Skirmish” • “Spin the Wheel” • “What Lies Beneath” • “Everything Old is New” • “Night of the Comet”
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| Wasteland
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“Secrets of Nimbus” • “The Lost City of Paradise” • “Blind Men Tell All Tales” • “The Undying” • “A Fistful of Gorn” • “Installation 18”
(Still part of main episode progression for Romulan Republic players.)
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| Lost Dominion: The 2800
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“Lost Dominion” • “Second Wave” • “Of Bajor” • “Operation Gamma” • “Facility 4028” • “Boldly They Rode”
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| Cold War
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“Cold War (wrapper)” • “Cold Call” • “Out in the Cold” • “Cold Comfort” • “Cold Case” • “Cold Storage”
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| Delta Quadrant
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“Kobali Crisis Act I” • “Kobali Crisis Act II” • “Kobali Crisis Act III”
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| See also: Featured episode • Patrol • Removed Missions • Task Force Operation
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