Not pictured: 60% of the series, including a third alternate timeline.
Spock: You are assuming that Nero knows how events are predicted to unfold. The contrary - Nero's very presence - has altered the flow of history...thereby creating an entire new chain of incidents that cannot be anticipated by either party. Uhura: An alternate reality? Spock: Precisely. Whatever our lives might have been, if the time continuum was disrupted, our destinies have changed.
Dragon Ball Z has at least three of these, where the divergences were Future Trunks and Cell time traveling. Trunks can't actually Set Right What Once Went Wrong in his own timeline, but he can in an alternate timeline. After warning the alternate timeline about Androids 17 and 18, he ends up staying and training in order to fight against Cell. After the Cell Games, he takes the skills he's gained in the past back to his future and kills his world's versions of the Androids, as well as Cell when he appears. Both fans and official guidebooks have also speculated on the existence of a fourth timeline. According to Cell, he killed Trunks and stole his time machine because Trunks destroyed the androids Cell was supposed to absorb. Since the Future Trunks that the series focuses on knew when Cell would appear to kill him, the Trunks who was permanently killed and had this time machine stolen must have visited a timeline where Goku didn't die of a heart disease, but Cell never surfaced and the androids were presumably defeated somehow. The most accepted theory was laid out in one of the guidebooks, that Bulma built a remote control that was used to defeat the androids there and that Trunks took it back to his future to use there, too— since he never would have become strong enough to defeat them on his own without training for the Cell Games.
Code Geass has an alternate version of our history, wherein the American Revolution was defeated by the British Empire following Benjamin Franklin's defection to the British, while Napoleon conquered the British mainland and forced the royalty to move to America.
Mirai Nikki: Paradox. It actually turns out the be very important to the main timeline in the last chapter, however.
Steins;Gate is actually mostly about getting out of the so called Alpha timeline(s) and back into the original but so called Beta timeline(s). In the end they will get the possibility of the third timeline "behind the steins-gate.
The Spider-Girl series (and a few other less successful comics) takes place in the MC2 universe, which diverged from the main continuity after the Clone Saga. in this continuity, Spider-Man's daughter survives and becomes Spider-Girl in the future.
Or the point of divergence may be even further back, as later on it's revealed that Simon Williams (aka Wonder Man) died in issue 9 and was never resurrected.
Marvel tends to mess in and out of clones and alternate timelines, to the point where several characters have a modus operandi off of it.
One alternate Earth in the DCMultiverse was formed soon after Jason Todd died. Batman, stricken with grief, abandoned his Thou Shalt Not Kill policies and virtually eliminated crime worldwide.
The Pony POV Series is established as being an Alternate Timeline to the main series timeline. While originally tied to the 'heart-world', the universe diverged completely and became independent as of 'The Last Roundup'
In Equal And Opposite Attraction there is a massive divergence where Negi never stops teaching and Fate goes soul-searching. This kicks off the plot when Negi leaves Mahora to get his life in order
Explained in-story in Star Trek. The two Star Trek timelines diverge at Kirk's birth. In the Prime timeline, Kirk is born on Earth and the timeline proceeds how you remember it. In the new timeline, Kirk is born in space, his father is killed by Nero, and Vulcan is eventually destroyed so there is no point asking Spock-Prime on what's going to happen next since he has no idea either now.
Although his knowledge of things that predated Kirks birth but became important later or that originated elsewhere wouldn't have been affected. Things like the Doomsday Machine, Giant Space Amoeba, V'Ger, Khan's sleeper ship, the existance of the Borg and the Dominion, subspace damage caused by warp drives, the need for whales, and so on.
What the non-linear aliens in the Bajoran wormhole or the Q must think of all this is probably best left for fan fiction.
The Godzilla series has done this several times to the point where each of the movies from Godzilla 2000 and onward (with the exception of the two with Mechagodzilla) are their own continuity branching off from the original.
In Triangle Jess gets stuck in a Groundhog Day Loop of her co-passengers getting killed by a masked killer. The first Jess tries to break the chain by meeting the Jess from the next loop. This creates a new timeline where the other passengers died differently by getting killed by a different masked killer. Subverted in that the two timelines play off at the same time and each influence each other. For example the new timeline eventually causes the second Jess to have her own story, which we don't see, where she eventually killed some of the passengers as the second masked killer which eventually made the first Jess turn into the first masked killer
In Sliding Doors, the movie shows two alternate timelines. The story starts off with the Main Character getting fired, while her boyfriend is cheating on her. The Main Character goes home, and either just catches the subway in time, finding her boyfriend in bed with another woman, or misses the subway, causing some other events to happen which means she arrives home after the other woman has left. The movie then alternates between the two story lines.
It's almost certain that there are two continuities in the original Planet of the Apes franchise. The first is the continuity that led to the society of the original film, possibly as described by Cornelius to the committe in Escape. The second is the altered continuity that the birth of their son, Caesar, sparked. It appears that the ape revolution was greatly sped up with his arrival. However, fans are split as to whether the continuities ultimately re-merge when history reaches the point where the original film was set, and humans will again end up mute wild animals and the world destroyed by the Alpha-Omega bomb or whether history was changed for good by the end of 'Battle' and Caesar forged a new future. The editing of 'Battle' didn't help things, the theatrical release had a hopeful tone, but the unedited version on most DVD releases clearly sets up the beginnings of the mutant society of 'Beneath'. The TV series likely exists in one of these continuities somewhere, while the animated series, Planet 2001 don't, and and Rise may or may not. 'Rise' is a Continuity Reboot, but there have been statements by the PT Bs contradicting that and painting it as a prequel as well.
Doc: Obviously, the time continuum has been disrupted creating this new temporal event sequence, resulting in this alternate reality. Marty: English, Doc. Doc: Here, here-here. Let me illustrate. (He moves aside cardboard boxes to set up his chalkboard) Doc: Imagine that this line represents time. 1985...the future...the past. Prior to this point in time, somewhere in the past, the timeline skewed into this tangient, creating an alternate 1985. Alternate to you, me, and Einstein, but reality for everyone else.
The Gary Paulsen book Hatchet ends with Brian being rescued. However, in the third book, Brian's Winter, it takes place in an alternate series of events where Brian has to survive through the winter. Of course, those spoiler tags are almost useless since they spoiled this on the back of the book.
The Black Trillium novel was co-written by three authors, who each went on to write a sequel (or two), effectively spawning three mostly incompatible timelines from a single root.
The book, The Wastelands of Stephen King's The Dark Tower series involves alternate timelines created in the previous book, The Drawing of the Three when Roland creates a paradox by saving the life of Jake in his own world, preventing him from travelling to Roland's world, and them ever meeting. The alternate timelines created, one where he travelled with Jake, and one where he was alone, slowly drive both Jake and Roland insane as their minds simultaneously believe both series' of events to be true.
Dinoverse has a vast number of alternate universes, but it's implied that the peaceful utopian Dinoverse, which has a present-day society of, well, dinosaurs, is the result of characters in the Mesozoic era rescuing an unusually smart Deinonychus from certain doom. There's still the heroes' reality with human civilization, and there are human and dinosaur versions of several characters.
Terminator: The Sarah Connor Chronicles branches off from the movie continuity after T2: Judgement Day - Sarah and John Connor leap through time from 1999 to 2007, skipping Sarah's death from cancer in 2002 and the date at which Judgement Day would have happened if Rise of the Machines were canon. Terminator Salvation, on the other hand, carries on from the Rise of the Machines continuity.
Lampshaded in EUReKA, where Henry explains to Sheriff Carter exactly why they can't accurately predict the future after hitting the Reset Button on the past five years to undo Henry meddling to keep his wife from dying in the past, since the differing actions alone will cause a Ripple Effect to make the timelines gradually diverge. And then something different happens.
It should be noted that Eureka has gotten twoAlternate Timeline treatments. The first one (mentioned above) only lasted an episode before being reverted; the second one, however, became the permanent timeline for the show.
The Malcolm in the Middle episode Bowling played with this, the divergence being which parent took the kids bowling instead of staying at home. The conclusion?
It's also worth noting that, according to the time-sensitive Observers, the first three seasons already took place in an Alternate Timeline that was thrown off-course from what was supposed to happen by the actions of an Observer. The Alternate Timeline of season 4 is probably a lot closer to how the original timeline was supposed to run.
The Community episode "Remedial Chaos Theory" explores 6 alternate timelines, each different depending on which number Jeff rolls on the Yatzee die. We then see the main timeline, which is where Abed catches the die instead of letting it roll.
The series flashes over to the "Darkest Timeline" every now and then to see how things are going (or at least Abed does in his own mind).
The episode with the two model U.N.s also used this explanation (at Abed's insistence) to explain the presence of two Earth's each with their own U.N.. Ultimately, it's integral to how the study group wins the competition.
The Scrubs episode My Butterfly, where the cast explored what different events resulted from a butterfly landing on an attractive woman's chest or alternatively, an unattractive man's chest. Ultimtely subverted in that the patient ends up dying in both timelines.
A few later episodes of Farscape see John Crichton exploring a few of these, particularly as interdimensional wormholes and the associated wibblie-wobblies become more important to the plot.
When Dallas retconned a whole season that had been unpopular with fans as All Just a Dream, the producers of the Spin-OffKnots Landing didn't want to retcon plots that had been influenced by events in that season, causing the show to split off as an Alternate Timeline.
BIONICLE had at least four different parallel timelines. For instance, in Dark Mirror, Takua was killed by a Toa of Iron, and in The Kingdom universe, as well as the universe briefly seen at the end of Brothers in Arms, he never became a Toa at all. He is a Toa in the main universe.
Star Trek has been indulging in a "Myriad Universes" series of books and comics which explores countless other realities throughout every Star Trek series, based on various differences in their timelines. Some vary hugely from the original, while others vary in slightly simpler ways. There's also the original Mirror Universe.
Much of the temporal nastiness in Chrono Cross is the result of two alternate futures clashing in the world's distant past. It's complicated.
Dark Cloud and it's sequel. The first game created a different timeline entirely by stopping the Dark Genie from ever coming to existence. The second game was mostly about this, you had to restore Origin Points (Event in past which influences future), it even creates new innovations in the future such as Aeroharmonic technology and Paznos' Colossus Mode which never existed before.
The main premise of the Half-Life mod series "Timeline." Rogue Black Mesa scientists have discovered how to use the dimensional portals to permit time travel, and have been messing with and creating new timelines. Eventually this technology falls into the hands of Those Wacky Nazis...
The Mega Man metaseries has one, expanded on in Mega Man Battle Network. Both Doctors Light and Wily presented their research to the government: network and robotics, respectively. In the world where Light's network research won out, the Battle Network and Mega Man Star Force games take place. However, when Wily's robotics were chosen instead, it led to the other series.
Ghost Trick has an in-game instance: the first timeline is a Bad Future where everybody dies, Missile is unable to save them due to lacking the needed ghost tricks, and Sissel refuses to help Missile due to only being concerned about his own quest for identity. At the end, Missile uses Yomiel's no-longer-immortal body to travel back in time 10 years to the Tesmik Park incident and wait out those ten years until that night returns. Then starts the second timeline, which is the Bad Future again, but diverging when Sissel awakens and Missile from the first timeline guides him under the guise of Ray, making Sissel think he's a blond-haired man in red instead, so that he'll naturally save Lynne and everyone else that could be a lead in his quest for identity due to said man's interactions with them. The third timeline begins after Sissel, Missile from the second timeline, Yomiel, and Detective Jowd go back 10 years again like the original Missile did and Set Right What Once Went Wrong by saving Yomiel's life and thus preventing his Start of Darkness, undoing the first two timelines and the first Missile's existence in the process.
The Babylon Project campaign "The Earth-Brakiri War" is set in an alternate 2260 where Babylon 5 had been destroyed and Earth had alienated itself from the other races due to a failure of diplomacy.
The existence of one of these and the desire of certain oddfactions to bring it back fuels the plot of Persona 2.
Surprisingly this is present in the Metal Gear series: Metal Gear Ghost Babel takes place in an alternate timeline where neither the events of the second game nor the events of the Solid series have taken place.
The Halloween Hack takes place after Earthbound. This time, the Chosen Four didn't return since they were sent to a timeline created when Giygas was killed in the past. Andonuts went mad with grief and became a serial killer because he thought he killed them.
Worm takes place on Earth Bet, which diverged from our timeline in 1982 with the appearance of Scion, the first superhero. Other worlds exist with their own divergent timelines — Earth Aleph being one.
In the South Park Episode "Go God Go!", Cartman uses a phone that can call homes in other time periods, even the commercial for it states that it is only for prank phone calls.
The end of Scooby Doo Mystery Incorporated has the Gang force history to reset itself in a much more pleasant direction after Scooby kills the Nibiru Entity. Harlan Ellison tells them that this isn't the first time that they've had their timeline rebooted either.