Alternate timeline

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An alternate timeline was a reality that diverged from the "true" timeline due to the actions of time travellers or other temporal phenomena. They were different from parallel universes in that they did not separate cleanly at the point of creation resulting in the new timeline destroying the old one. (PROSE: Imperial Moon) The phenomenon may also have been described as an "interstitial spillage of time." (AUDIO: Project: Lazarus) Alternate timelines constantly winked in and out of existence with every decision made. (AUDIO: The Wrong Doctors)

Physics

Alternate timelines could be visited accidentally by jumping a time track (TV: The Space Museum, AUDIO: The Mutant Phase) or contacting other anomalies (AUDIO: Colditz) in the Time Vortex. Deliberate travel to these timelines was possible if the traveller possessed something, such as the sigil ring, that allowed them to change time streams. (PROSE: Goth Opera)

They may have diverged from points in history when there was temporal fluctuation. The power required to adjust the timeflow and overcome temporal inertia on such a scale couldn't fit on a single planet, but beings with enough power were capable of doing so, such as Sutekh, the Guardians of Time, Rassilon, and the Chronovores. Even the Doctor or the Master could have the know-how or inclination to create them. Because the universe only had a finite amount of mass and energy to exist as one universe, the creation of an alternate timeline adversely affected the real timeline, causing chaos throughout the universe; releasing enough energy could destroy the timeline and set history back on its correct course. (PROSE: Blood Heat)

Though a timeline could be negated, memories of it could still be retained. (TV: The Big Bang, The Impossible Astronaut) Sometimes these memories were subconscious and only surfaced in dreams. (AUDIO: The Time of the Daleks, Jubilee)

Metaphysics

From a metaphysical viewpoint, alternate timelines were always being extinguished as fewer and fewer choices became open. This was particularly affected by time travellers who changed the future whenever they arrived in a new time. This was the cosmic pain of the universe and in this manner Gabriel and Tanith were personifications of the timelines that never existed. (PROSE: Falls the Shadow)

The existence/creation of alternate timelines and parallel universes were held in check by the existence of the Time Vortex, which was sustained by the existence of the Time Lords. (PROSE: The Domino Effect)

Terminology

The phrase "alternate/alternative timeline/universe" was sometimes used interchangably with "parallel universe"; however, alternate timelines usually changed after a single moment in time, whereas parallel universes usually had more than one difference from the "normal" universe.

Timelines encountered by the Doctor

Timeline Negated By Featured in
The First Doctor and his companions became exhibits in the Moroks' Space Museum First Doctor, Ian Chesterton, Barbara Wright, and Vicki TV: The Space Museum
Barbara Wright married Ptolemy I and became Queen of Alexandria Alternate Barbara PROSE: The Book of Shadows
WOTAN conquered Earth (this was the correct timeline before it was changed by the Doctor) First Doctor PROSE: The Time Travellers, TV: The War Machines
1794 Earth became the World Machine, with the French Revolution continuing until 1804 The Pageant after being confronted by the First Doctor PROSE: The Man in the Velvet Mask
Mechanistria was taken over by machines possibly negated by Drako, though he might not have succeeded PROSE: Peril in Mechanistria
Nancy Grover used Grold technology to become a goddess Third Doctor and Liz Shaw PROSE: The Eye of the Giant
The Power Elite took over Earth Third Doctor PROSE: Prisoners of the Sun
Freedom fighters from the 22nd century assassinated Sir Reginald Styles, causing a war which enabled the Daleks to invade Earth Third Doctor and Jo Grant TV: Day of the Daleks
Theodore Cassells's experiments led to a global war which devastated Earth Third Doctor COMIC: A Stitch in Time
The Third Doctor died on Dust and regenerated Eighth Doctor by destroying Gallifrey (PROSE: The Ancestor Cell) PROSE: Interference - Book One, Interference - Book Two
Sutekh was freed in 1911 and devastated Earth Fourth Doctor and Sarah Jane Smith TV: Pyramids of Mars
Daleks underwent the Mutant Phase Dalek Emperor AUDIO: The Mutant Phase
Melanicus created the Millennium Wars Fifth Doctor, Sir Justin, and Shayde COMIC: The Tides of Time
The 22nd century Dalek invasion didn't take place Fifth Doctor and Nyssa AUDIO: Renaissance of the Daleks
Earth in 2008 was controlled by smoke creatures Fifth Doctor, Nyssa, and Thomas Brewster AUDIO: The Haunting of Thomas Brewster
Adric created a city of intelligent scorpions Fifth Doctor and Nyssa AUDIO: The Boy That Time Forgot
Phil and Trev created a perfect world Fifth Doctor, Nyssa, and Thomas Brewster AUDIO: A Perfect World
John Smith and the Common Men were the most successful band in the world instead of the Beatles Fifth Doctor and Nyssa AUDIO: 1963: Fanfare for the Common Men
Walter Raleigh went back in time and encountered aliens Sixth Doctor AUDIO: Voyage to the New World
The Doctor's arrival on the planet Bixor to investigate the cause of its destruction, turned out to be the actual cause of its destruction Sixth Doctor AUDIO: The Wings of a Butterfly
The Herd-Leader of the Bovine travelled back in time to warn himself he shouldn't help Columbus discover America Perpugilliam Brown and Christopher Columbus AUDIO: Trouble in Paradise
Cyberverse Possibly negated when Evelyn Smythe left the Sixth Doctor WC: Real Time/AUDIO: Real Time
Daleks invaded Earth in 1903 and were defeated by the British Empire the last surviving Dalek AUDIO: Jubilee
Wolfgang Amadeus Mozart became immortal Sixth Doctor and Evelyn Smythe AUDIO: My Own Private Wolfgang
President Bailey allowed the Slithergee race to settle on the first moon of the planet Puxatornee in the year 3060, which allowed the Slithergee to take complete control of the planet in the year 3090 Seventh Doctor, Mel, Stuart, and Reed AUDIO: Flip-Flop
The assassination of President Bailey caused the next President, Mitchell, to declare war on the Slithergee race in the year 3060, the result of which left the planet Puxatornee devastated by the year 3090 Seventh Doctor, Mel, Lieutenant Stuart, and Lieutenant Reed AUDIO: Flip-Flop
Alternate timeline (The Ripple Effect) Seventh Doctor PROSE: The Ripple Effect
Humans evolved into Haemovores Seventh Doctor and Ace TV: The Curse of Fenric
The Dark Matrix terrorised England Seventh Doctor and Ace PROSE: Matrix
The Nazis won World War II after a piece of laser technology was left at Colditz Castle Alternate Eighth Doctor and Elizabeth Klein (inadvertently) AUDIO: Colditz, Klein's Story
Vladimir Kryuchkov succeeded Konstantin Chernenko as leader of the Soviet Union, causing World War III to occur in 1989 Seventh Doctor AUDIO: Protect and Survive
Adolf Hitler used the Timewyrm's power to enable Nazi Germany to conquer Earth Seventh Doctor and Ace PROSE: Timewyrm: Exodus
Chad Boyle killed Dorothy McShane with a brick to the head Ace PROSE: Timewyrm: Revelation
The Process enslaved the Time Scaphe crew Seventh Doctor PROSE: Cat's Cradle: Time's Crucible
Silurian Earth Destroyed, not negated, by Seventh Doctor PROSE: Blood Heat
Brigadier Lethbridge-Stewart was shot and killed by a Vardan in 1976 Artemis the Chronovore PROSE: No Future
Alternate timeline (Time & Time Again) Seventh Doctor, Ace, and Bernice Summerfield COMIC: Time & Time Again
The Knights of Velyshaa conquered Gallifrey Fifth Doctor, Sixth Doctor, Seventh Doctor, and the Temperon AUDIO: The Sirens of Time
Elizabeth Klein created the Galactic Reich after stealing the Doctor's TARDIS and making repeated corrections to the timeline Seventh Doctor, Elizabeth Klein, and the Selachians (the last two inadvertently, after being manipulated by the Doctor) AUDIO: The Architects of History
Earth was destroyed by the Eye of Harmony Eighth Doctor and Grace Holloway TV: Doctor Who (TV story)
Edward Grove came to life Eighth Doctor and Charley Pollard AUDIO: The Chimes of Midnight
Sebastian Grayle became immortal and helped the Nimon conquer Earth Eighth Doctor and Charley Pollard AUDIO: Seasons of Fear
Shakespeare vanished from history Eighth Doctor and Charley Pollard AUDIO: Invaders from Mars (audio story), AUDIO: The Time of the Daleks
Daleks invaded Earth in the 17th century Eighth Doctor and Charley Pollard AUDIO: The Time of the Daleks
The Master used a conceptual bomb made from Bob Dovie's refusal to accept the existence of the Doctor's TARDIS to erase said TARDIS, thus meaning the Doctor never left Gallifrey First Doctor, Second Doctor, Third Doctor, Fourth Doctor, Fifth Doctor, Sixth Doctor, Seventh Doctor, and Eighth Doctor AUDIO: The Light at the End
Humans didn't evolve and Earth was a Tractis colony known as Paratractis Eighth Doctor, Sam Jones, and Jo Grant PROSE: Genocide
Sato Katsura formed the Church of the Glorious Dead which conquered Earth Kroton COMIC: The Glorious Dead
Morbius returned and defeated the Time Lords Eighth Doctor AUDIO: Vengeance of Morbius
Straxus became Kotris and helped the Dalek Time Controller Straxus AUDIO: Dark Eyes
Pete Tyler didn't die and Reapers began consuming humanity Pete Tyler TV: Father's Day
The Year That Never Was Tenth Doctor, Martha Jones, and Captain Jack Harkness TV: Last of the Time Lords
Donna's World alternate Donna Noble, with assistance from Rose Tyler TV: Turn Left
The Progenitor Daleks repopulated Skaro and exterminated humanity to extinction in 1963 Eleventh Doctor and Amy Pond GAME: City of the Daleks
The Kin gained control of Earth meaning humanity was extinct in 2010 Eleventh Doctor PROSE: Nothing O'Clock
The Doctor's TARDIS exploded, creating Cracks in Time which began erasing the universe's history Eleventh Doctor, Amy Pond, Rory Williams (Auton), and River Song (TV: The Big Bang) TV: Series 5
Ship kidnapped people and wiped Foxtown off the map Eleventh Doctor PROSE: The Way Through the Woods
Amy Pond was stranded on Apalapucia for 36 years Eleventh Doctor and Rory Williams TV: The Girl Who Waited
River Song's World Eleventh Doctor, Amy Pond, Rory Williams, River Song, and the Teselecta TV: The Wedding of River Song
The Silurians attempted to pump poison onto Earth's surface to reclaim it Eleventh Doctor and River Song GAME: The Eternity Clock
The Progenitor Daleks invaded and destroyed London in or before 2106 Eleventh Doctor and River Song GAME: The Eternity Clock
Amy Pond was killed by Jack the Ripper Eleventh Doctor COMIC: Ripper's Curse
The Cybermen conquered the galaxy Eleventh Doctor and Jean-Luc Picard COMIC: Assimilation²
Rory Williams remained imprisoned in Winter Quay for the rest of his life Rory Williams and Amy Pond TV: The Angels Take Manhattan
The Creevix erased the existence of Guy Taylor, allowing them to use his time machine to enter the universe on the 23rd of November, 2013 and consume it First Doctor, Susan Foreman, Second Doctor, Jamie McCrimmon, Zoe Heriot, Third Doctor, Mike Yates, Fourth Doctor, Romana II, Fifth Doctor, Adric, Nyssa, Tegan Jovanka, Sixth Doctor, Peri Brown, Seventh Doctor, Ace, Eighth Doctor, Charley Pollard, Ninth Doctor, Rose Tyler, Jack Harkness, Tenth Doctor, Donna Noble, Eleventh Doctor, Alice Watson, and Cedric Chivers AUDIO: The Time Machine
The TARDIS was damaged by van Baalen Bros. and self-destructed Eleventh Doctor TV: Journey to the Centre of the TARDIS
The Great Intelligence negated the Doctor's victories Clara Oswald TV: The Name of the Doctor
Gallifrey and the Time Lords are destroyed by the Doctor with The Moment The First Doctor, Second Doctor, Third Doctor, Fourth Doctor, Fifth Doctor, Sixth Doctor, Seventh Doctor, Eighth Doctor, War Doctor, Ninth Doctor, Tenth Doctor, Eleventh Doctor and the Twelfth Doctor TV: The Day of the Doctor
The Doctor dies on Trenzalore Clara Oswald and the Time Lords TV: The Time of the Doctor

Timelines encountered by others

Timeline Negated By Featured in'''
The Seventh Doctor defeated the Vardan invasion of Earth by leaving clues for his past self The Monk PROSE: No Future
Insects of the Mind evolved as the dominant life on Earth The existence of time travel PROSE: Falls the Shadow
Britain was a conformist republic The existence of time travel PROSE: Falls the Shadow
Andrea Yates' World alternate Andrea Yates TV: Whatever Happened to Sarah Jane?
The Trickster's World Eddie and Barbara Smith TV: The Temptation of Sarah Jane Smith
Ship erased Sarah Jane Smith, Luke Smith and Clyde Langer Adam Lloyd and Rani Chandra TV: The Mad Woman in the Attic
Deindum from the future conquered the galaxy Bernice Summerfield PROSE: Present Danger, AUDIO: Escaping the Future