| Cross-faction episodes in Star Trek Online
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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
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| Lost Dominion
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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 • Cold Call • Out in the Cold • Cold Comfort • Cold Case • Cold Storage
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| Romulan Mystery
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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 • (Venture into Deep Space) • (Badlands) • (Suspect) • (War Games) • (Shutdown) • (Rapier) • (Forging Bonds) • (The Long Night) • (The Tribble with Klingons) • (Tear of the Prophets) • (Crack in the Mirror) • (Seeds of Dissent) • (The Other Side) • (Cage of Fire)
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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 • (Collateral Damage) • (Asset Recovery) • (State of Q) • (The Return) • (A Light in the Dark)
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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 • Know Your Enemies • The Kobali Front • Capture the Flag • The Dragon's Deceit • Alliances • Better with Friends • Revolution • Taking Care of Enemies • Takedown • What's Left Behind • Dust to Dust • (With Friends Like These...)
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| Kobali Crisis Act I
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The Cavalry • The Son • The Temple of My People • Data Recovery
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| Kobali Crisis Act II
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Looming Shadows • Hidden Assault • A New Warfare
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| Kobali Crisis Act III
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Breaking the Wall • With Our Last Breath • Our Chance for Peace
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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 • Warriors of the Empire • A Day Long Remembered
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| Terran Gambit
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Firewall • Red Shift • Blue Shift • The Calling • Eye of the Storm • The Fujiwhara Effect
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| Kings & Queens
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Wish Upon A Star • Taken By Surprise • Scorpion's Abyss • Situation Under Control • Axiom • All That Matter • Best Laid Plans • Curse of Phrygia
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| Task Force Operations
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Starbase Fleet Defense • Fleet Alert • Fleet Transport Defense • Starbase Incursion • Romulan Imperial Minefield • Crystalline Catastrophe • Colony Invasion • Arena of Sompek • Kobayashi Maru • Infected: The Conduit • Infected: Manus • Cure Applied • Cure Found • Khitomer Vortex • Khitomer in Stasis • Into the Hive • Hive Onslaught • Transdimensional Tactics • Self Destructive Tendencies • Azure Nebula Rescue • Vault: Ensnared • Vault Shuttle Event • Atmosphere Assault • Defend Rh'Ihho Station • Storming the Spire • Breach • Undine Assault • Undine Infiltration • Viscous Cycle • Borg Disconnected • Bug Hunt • Battle of Korfez • Brotherhood of the Sword • Gateway to Gre'thor • Herald Sphere • Counterpoint • Operation Wolf • Iuppiter Iratus • Bird Cage • Leviathan • Storm Chasers • Forged in Fire • Days of Doom • Battle of Procyon V • Miner Instabilities • Gravity Kills • Tzenkethi Front • Dranuur Beach Assault • Dranuur Gauntlet • Binary Circuit • Core Assault • Twin Tribulations • Swarm • Battle at the Binary Stars • Best Served Cold • Defense of Starbase One • Mycelial Realm • Operation Riposte • Pahvo Dissension • Peril Over Pahvo • Remain Klingon • To Hell with Honor • Devil's Heart • Shattered Peace • Belly of the Beast
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| Patrols
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Blockade Runner • Wanted • Tempting Targets • Aftermath • Unity • Gone Dark • Preying Upon the Weak • Satellite Defense • Showdown • Rescue and Search • Ruins of Doom • Sentinels • The Ninth Rule • Within The Briars • To Die with Honor • Clash Above Ceron • Strike at Seedea • Trouble Over Terrh • Redemption Over Qu'Vat • Jailbreak at Rura Penthe • Jupiter Station Showdown • Khonshu Khaibit • One Night in Bozeman • Skeleton Crew • Witches Brew • (Borg Battlefield Patrol) • (Ocampan Freighter Patrol) • (Sakari System Patrol) • (Trakia System Patrol) • (Shivolia System Patrol) • (Orendal System Patrol) • (Parein System Patrol) • (Nanipia System Patrol) • (Kendren System Patrol) • (Legira System Patrol) • (Rivos System Patrol) • (Hodos System Patrol) • (Ram Izad System Patrol) • (Xiokel System Patrol) • (Wyanti System Patrol) • (Pansarka System Patrol) • (Tekara System Patrol) • (Gerren System Patrol)
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| Seasonal
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Hearts and Minds • Cat's Tale
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| Missions in parentheses are no longer available as of the current version of Star Trek Online.
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