Story arc

Listed below are various story arcs that have featured within Doctor Who canon, 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
Classic Revival
 * Season 16 - The Key to Time
 * Season 18 - Journey in E-Space - (Full Circle, State of Decay & Warriors' Gate)
 * Season 18/Season 19 - The Return of the Master/ New Beginnings - (The Keeper of Traken, Logopolis & Castrovalva)
 * Season 20 - The Black Guardian - (Mawdryn Undead, Terminus & Enlightenment)
 * Season 23 - The Trial of a Time Lord
 * Series 1 - Bad Wolf meme
 * Series 2 - Torchwood Institute
 * Series 3 - Harold Saxon
 * Series 4 - Medusa Cascade, Disappearing Bees, Lost Worlds, The Return of Rose, Prophecies and Bad Wolf
 * 2009 Specials - Tenth Doctor's Regeneration
 * Series 5 - Cracks in Time

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

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

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

Big Finish Bernice Summerfield Series
to be added

Torchwood television stories

 * Series 2 - The Ressurection of Owen Harper - Reset, Dead Man Walking & A Day in the Death