Story arc

Listed below are story arcs that have featured in Doctor Who canon. They are presented in order of story, season or series production, which then lists the story arc present throughout those stories, season or series.

Doctor Who television stories

 * Season 8 - The Master arc
 * Season 16 - The Key to Time
 * Season 18 - Journey in E-Space
 * Season 18/Season 19 - The Return of the Master/ New Beginnings
 * Season 20 - The Black Guardian
 * Season 23 - The Trial of a Time Lord
 * Series 1 - The Bad Wolf meme
 * Series 2 - The Torchwood Institute
 * Series 3 - Harold Saxon ("You Are Not Alone")
 * Series 4 - The Medusa Cascade, disappearing bees, lost worlds, the return of Rose
 * 2009 Specials - Tenth Doctor's regeneration ("He will knock four times")
 * Series 5 - Cracks in Time, the Pandorica, the Silence
 * Series 6- The Silence, Kovarian, Eleventh Doctor's death, Amy's pregnancy, River Song's identity
 * Series 7- The Question, Clara Oswald's identity

Virgin New Adventures

 * Timewyrm: Genesys, Timewyrm: Exodus, Timewyrm: Apocalypse, Timewyrm: Revelation - Timewyrm arc
 * Cat's Cradle: Time's Crucible, Cat's Cradle: Warhead, Cat's Cradle: Witch Mark - Cat's Cradle arc
 * Blood Heat, The Dimension Riders, The Left-Handed Hummingbird, Conundrum and No Future - Alternate Universe arc
 * Sleepy, Christmas on a Rational Planet, Cold Fusion, The Death of Art, Damaged Goods and So Vile a Sin - Psi Powers arc

BBC Eighth Doctor Adventures

 * Alien Bodies, Unnatural History, Interference - Book One, Interference - Book Two, The Taking of Planet 5, The Shadows of Avalon, The Ancestor Cell - Time Lords' future war with The Enemy
 * Longest Day, Legacy of the Daleks, Dreamstone Moon, Seeing I - Looking for Sam
 * The Ancestor Cell, The Burning, Casualties of War, The Turing Test, Endgame,Father Time, Escape Velocity - Lost memory and second exile in Earth.

Big Finish Adventures

 * Zagreus, Scherzo, The Creed of the Kromon, The Natural History of Fear, The Twilight Kingdom, Faith Stealer, The Last, Caerdroia, The Next Life - Divergent Universe arc
 * Patient Zero, Blue Forgotten Planet, Mission of the Viyrans, Urban Myths, Urgent Calls, I.D., The Wishing Beast, The Vanity Box - Virus Strain arc

The New Eighth Doctor Adventures

 * Blood of the Daleks, Human Resources, Grand Theft Cosmos, Worldwide Web - Headhunter saga
 * Situation Vacant, Nevermore The Book of Kells, The Resurrection of Mars, Lucie Miller, To the Death - The revenge of the Time Meddler.

Doctor Who Magazine comic strips

 * Voyager, Polly the Glot, Once Upon a Time Lord - Task for Voyager

Virgin Bernice Summerfield New Adventures

 * Where Angels Fear, The Mary-Sue Extrusion, Dead Romance, Return to the Fractured Planet, Twilight of the Gods - Dellahan gods arc

Torchwood television stories

 * Series 2 - The Resurrection of Owen Harper, Jack's past, John Hart
 * Series 3 - Children being controlled by the 456
 * Series 4 - Miracle Day

Trilogies
Similar to the "Story Arcs" but consisting of 3 stories, some in books, some in episodes and others in "Audio stories".

In books

 * MA: The Scales of Injustice, PDA: Business Unusual, PDA: Instruments of Darkness - C19 Trilogy

In audio play

 * The Reaping, The Gathering, The Harvest: Cybermen Trilogy.
 * The Judgement of Isskar, The Destroyer of Delights, The Chaos Pool: The Key 2 Time Trilogy
 * Project: Twilight, Project: Lazarus, Project: Destiny: The Forge
 * City of Spires, The Wreck of the Titan, Legend of the Cybermen: The Land of Fiction
 * Protect and Survive, Black and White, Gods and Monsters: The Black TARDIS

In TV series

 * The End of the World, New Earth, Gridlock: The Face of Boe
 * Resurrection of the Daleks, Revelation of the Daleks, Remembrance of the Daleks: The Dalek Civil War Trilogy