Alternate timeline

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 was also described as an "interstitial spillage of time." (AUDIO: Project: Lazarus)

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)

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, 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
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
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
Daleks were peaceful	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, 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 and Elizabeth Klein and the Selachians (both inadvertently after being manipulated by the Doctor)	AUDIO: The Architects of History
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
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, Jo Grant	PROSE: Genocide
Sato Katsura formed the Church of the Glorious Dead which conquered Earth	Kroton	COMIC: The Glorious Dead
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 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	TV: The Girl Who Waited
River Song's World	Eleventh Doctor, Amy Pond, Rory Williams, River Song, 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, Amy Pond	TV: The Angels Take Manhattan
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	TV: The Name 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	TV: The Mad Woman in the Attic
Deindum from the future conquered the galaxy	Bernice Summerfield	PROSE: Present Danger, AUDIO: Escaping the Future