An example of a Retcon caused by forces within the story itself, usually using Time Travel of some sort to alter history. Rarely is it used purely as a dramatic device; the real function is to paper over continuity gaps and mistakes.
For example, let's say that the author of a novel series was dissatisfied at the way she'd killed off a character in an earlier book. Instead of just having him show up and explain that he was Only Mostly Dead, she has the other characters pulled back in time by an evil plan of the Big Bad; in the process, they manage to prevent the events that lead to death of the character, and when they get back, ta-da! There he is, good as new.
Whether or not characters will remember the pre-retconned state depends on the story.
Often (especially lately), Cosmic Retconning is the go-to method for demolishing Continuity Lock-Out and drawing in a younger audience. As a rule of thumb, superhero movies are the hottest way to increase readership; thus, the new canon should conform to whatever is playing in theaters or on television. See also Ret Canon.
A potential downside to this trope, of course, is that it can invoke a strong sense of Shoot the Shaggy Dog on previous stories in the franchise. Moreover, if the old versions of the characters see the end coming for their world and realize that, at best, they can only save the universe by drastically changing it (perhaps erasing countless people from existence and rewriting the personalities of the survivors), the results can be pure Nightmare Fuel — and also possibly a source of severe Mood Whiplash if either the outgoing or incoming universe is notably more "carefree and innocent" than the other.
Note that this applies only to actual retcons; something like Back to the Future, where changing the past is part of the original thrust of the story, doesn't count.
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Anime and Manga
Transformers, of course, has one of its own: the Unicron Singularity, which ripped and tore at the fabric of time and space in a way that essentially opens up a planet-sized plot hole just to make room for itself to fill it.
The Unicron Singularity didn't exist as this at first, and it was transformed into one by the club comic writers to account for some (admittedly minor) inconsistencies between Transformers Energon and Transformers Cybertron. Mind you, these are only minor in comparison to the humongous plot holes that already populated the rest of the entire Transformers multiverse, which did not have such a black hole.
There actually exists a transformer, Vector Prime, who was tasked by Primus to protect the stability of the timeline- in other words, the number of plot holes in Transformers is so bad, it is actually an in-universe threat, and there needs to be someone to keep the holes and inconsistencies from destroying everything. He does his best to fix things (usually retconning them from outside the timeline to cover inconsistencies, but coming in person for tremendous holes like the Singularity) so presumably any inconsistency we see was simply recorded before he got around to it, and our media are ripple effect proof.
Played for laughs in Excel♥Saga, where the Great Will of the Macrocosm has to reset the plot multiple times per episode.
Done several times throughout the backstory of Xxx Ho Lic and Tsubasa Reservoir Chronicle. You'd need a diagram drawn by M.C. Escher in seven dimensions to figure out the order of which retcon came before which, though. Altogether, they produced several clones, eliminated the royalty of a kingdom as royalty while leaving their children the prince and princess in place (their ancestor from another dimension had to come in to act as a placeholder and keep causality intact), caused reality to not notice that someone had died for several hundred years, at which point it had always noticed (except for the aforementioned clones and friends), and both added and removed the main character's parents from existence (their existence in-story predated the retcon somehow, and the protagonist managed to survive his parents ceasing to have ever existed via a Deal with the Devil).
Stone Ocean, the sixth story arc of JoJo's Bizarre Adventure, ends with the antagonist Enrico Pucci recreating the universe. The next story arc, Steel Ball Run, is a Continuity Reboot that takes place in the same time period as the first story arc, Phantom Blood.
At the very end of the Neon Genesis Evangelion manga, Shinji rejects Instrumentality and causes the Reset Button to be hit. The final chapter takes place in the rebooted timeline, where the Earth is safe, Second Impact never occurred, and the Angels never appeared on Earth.
Crisis on Infinite Earths did it to the entire DC Universe - the destruction of The Multiverse damaged the time-stream, changing the histories of many characters who lived on the only surviving Earth, thus removing their pre-Crisis backstories (and their campiest adventures.) Several survivors of other Earths have been rewritten into the new history. (For several years this failed to work properly with Power Girl, and she shifted between several conflicting origins until the universe found a way to slot her in properly. Or rather, that was the in-universe explanation for her Multiple Choice Past.)
Zero Hour: Crisis in Time, the first sequel to Crisis on Infinite Earths, was the second universe-wide retcon, caused by Hal Jordan and Hank Hall going mad and tampering with the timestream. It created the sliding timescale that the DCU has used since and altered the backstories of several characters, most notably Hawkman and the Legion of Super-Heroes.
In Infinite Crisis, CoIE's second sequel, a group of survivors from the pre-Crisis multiverse try to separate the numerous Earths yet again, leading to the multiverse's retroactive re-creation. It also featured a second, separate cosmic retcon; see below. (The third sequel, Final Crisis, did not radically alter continuity.)
The picture at the top of the page came from Infinite Crisis. Many of the changes here were caused by Superboy-Prime pounding on the walls of reality, giving rise to the "Superboy Punch!" meme as a way of hand-waving continuity errors.
Flashpoint, building off The Flash: Rebirth mentioned below, boils down to simply a time-traveller mucking things up and the heroes having to fix it. When The Flash makes the fixes, he's advised that the Vertigo Comics and Wildstorm continuities are fragments of the DCU and need to be merged into a single timeline. It seems to be this merging, not a case of incorrectly repairing history, that causes the retcons.
Marvel uses it less often, usually preferring the more "subtle" Sliding Timescale. This usually prevents the all-at-once changes of a Cosmic Retcon by feeding changes out gradually over decades.
Marvel had their own Superboy-Prime for a while in the form of Wanda Maximoff, the Scarlet Witch. When her powers shifted from "control of probability" to "able to reshape reality at will" and she went bugnuts crazy, "Wanda did it" became a very popular Hand Wave for a little while.
The creators of ElfQuest were forced to do this by Executive Meddling: basically, they lost the rights over a large group of characters, the Wavedancers, created as a spin-off by someone Running the Asylum. Because they did want to keep the overall story, a new group of Wavedancers was created in their place, and the original group was handwaved as a dream brought on by Big Bad Winnowill.
In The Sandman, Delirium threatened at one point to turn Mazikeen into a "a demon half-face waitress night-club lady with a crush on your boss", and "make it so you've been that from the beginning of time to now and you'll never ever know if you were anything else and it will itch inside your head worse than little bugses". Given that Mazikeen already was a demon with only half a face working at a night-club, it's unclear if Delirium actually did make a Cosmic Retcon (with the original state never being seen by the reader), or if she was just being her usual Cloud Cuckoolander self.
This is what happens if enough living creatures share the same dream. If a thousand cats were to dream of a world where they rule over humans then the universe would change so that it had always been that way. Luckily getting a thousand cats to agree to do the same thing is nigh impossible. Also, this is how humans came to rule the world.
Alan Moore's Supreme run starts with the main character finding out that he is not the only Supreme - reality has been revisioned multiple times in history, and all his previous incarnations (be they alternate counterparts, imagined versions or "future" selves) together with all their supporting characters, end up in the Supremacy, a dimension which they turned into a utopia. Later we find out that his Arch-Enemy Darius Dax has a similar thing - all his previous versions go to a dimension called the Daxia.
Much is made of the fact that Supreme (that is, the one starring in the book) survives the retcon in the first issue, though little of his history or characterization remains the same — a Lampshade Hanging of the fact that Moore's run is a retool or "soft reboot" of Rob Liefeld's material.
In The Flash: Rebirth, it is revealed that Barry Allen's mother is dead and his father, the only suspect, died in prison. For years Barry Allen was one of the few superheroes withouta traumatic origin and his parents grew up and old without complication; it turns out it is because Barry's archenemy, the Reverse-Flash, went back in time, killed his mom, and framed his dad.
J. Michael Straczynski's revamp of Wonder Woman has Diana not as the first woman to leave Themyscria and make her way in man's world, but as a survivor of a Themyscria that was sacked when she was a child and who is just now coming into her Amazon heritage. Other characters in the DCU (such as Max Lord) are stunned to find out that few people seem to remember Wonder Woman as she was. Diana's goal is to try setting things right. This revamp was a Gambit Pileup between the goddesses Nemesis and Clotho. Eventually Diana manages to set everything right, but her ordeal, likened to the Odyssea, was meant to introduce new changes into the status quo, like a revised outfit and an harder, no-nonsense attitude for Diana, though this too seems to have be retconned by the end of Flashpoint and into her new series. Wonder Woman's pants (and lack thereof) were the cause of so much drama that for several months they were in limbo, though by the time September 2011 rolled around she was again pantsless.
In the Sonic The Hedgehog comics, this happens in the Mobius: X Years Later reality (which is separate from the main canon universe). Damage to the fabric of reality from previous adventures threatens to completely destroy the timeline, so Sonic goes back in time to fix it, which results in reality changing - before, Mobius was a Utopia ruled by King Sonic, where all the villains were either dead or at peace with the heroes. But after the changes, it becomes a totalitarian dictatorship ruled by King Shadow and enforced by his Secret Police. Fortunately, the heroes who remember the way things are supposed to be come together and defeat him, returning things to the way they're supposed to be (albeit still with the alternate history).
There are also shades of this in Silver's stories; everytime he travels backwards in time, he causes small alterations to the timeline. Just not enough to undo the Bad Future he lives in.
Dr. Eggman attempts to invoke this trope in the Sonic: Genesis storyline - hooking up a Chaos Emerald to the Death Egg II, he attempts to rewrite history so that Sonic never existed... and ends up creating the video game universe instead, though with the Freedom Fighters and Snively with them. Sonic is able to go Super and, in an attempt to save Sally due to the fact that she was killed before the first Retcon, resets the universe to its normal state. However, because of that one change, a number of things about Mobius itself is altered.
Happens again in the Worlds Collide crossover with Mega Man, where Eggman and Dr. Willy recreate the Genesis Wave, this time affecting both their worlds. Though rather than trying to erase Sonic and Mega Man, they alter history so Mega Man is post-Mega Man 10 (allowing the use of Bass, Proto Man and Duo) and Sonic is in the modern video game setting rather than Archie's unique comic universe (for familiarity to non-Archie Sonic readers).
Doctor Strange has seen this happen a few times (being pals with Higher Beings will do this). In one storyline he saw the entire world destroyed and recreated except for himself, causing him some psychological distress as he wondered if the people he knew and loved were actually real.
In Raven Child's The Smurfette Village fanfiction series, the events that take place in the fourth story "A Home Through Time" retcon The Smurfs' ninth season (the time-traveling episodes) out of existence, setting things up for the events that take place in the story series proper.
The 2009 Star Trek movie has Nero traveling back in time and killing Kirk's father, radically changing the timeline, creating a brand new continuity.
Oh, and blowing up Vulcan, and killing Spock's mom. Can't forget that!
In the Mouth of Madness has some particularely mind-bending ones. The crux of the story is that horror writer Sutter Cane has become so powerful that his creations have become reality, and the protagonist John Trent finds himself in the fictional setting of his stories. By the time he gets back to the "real world" his partner Linda Styles has been written out by the writer (not even her boss, who sent them on their mission, can remember her), and Cane's reality-destroying novel was already delivered by Trent to the publishers and has been on the shelves for weeks, even though Trent just emerged from Hobb's End. The Cane that Trent encountered might also be an Author Avatar of the real Cane, who is writing the entire story of the movie (yes, the one you are watching), Cane might have been influenced by a monolith of Eldritch Abominations to change reality so they can transform it into something wholly alien, or Trent may be particularly insane.
Japanese time-travel movie Time Slip Yankee shows what happens when you mess with your parents first meeting Back to the Future-style. The main character is snap-backed into a retconned timeline where his then girlfriend in now his mother after his parents fell for different people. Everything about his life is different, even his body.
Thief of Time: History was literally shattered by a "glass clock" that trapped the Anthropomorphic Personification of Time, and then patched back together (albeit with some weird gaps and miscellaneous changes) by the History Monks; the plot of the book revolves around the History Monks stopping someone else from making a second clock. It's implied that this explains the prevalence of Schizo Tech on the Discworld and some of the continuity gaps from earlier books.
Mort: The Interface is the physical manifestation of the universe gradually retconning away Mort's 'mistake' in not taking Keli's life. More accurately, Mort changed how history is meant to go, and the Interface represents the inertia of history Cosmic Retconning it back again.
In the Warcraft universe, the book trilogy The War of the AncientsRetCons some parts of Azerothean history due to a few people going back in time (most notably the blue dragonflight going from extinct to having enough members to wage war against all other dragons and some mortals at the same time).
In the Dragonlance Legends books, much of the plot revolves around the efforts of various characters to Cosmic Retcon stuff they don't like in the past. Tasslehoff is central to this, because kender who travel through time can change the flow of events. First Tasslehoff tries to Retcon away the Cataclysm; Raistlin tricks him into breaking the time-travel device instead. Then Raistlin tries to Retcon away the death of Fistandantilus (since he himself has taken Fistandantilus's place in history), and succeeds, entering the Abyss instead of being blown to smithereens. Finally, Caramon and Tasslehoff wind up in a future where Raistlin wins, and return to the present in order to Retcon everything back to normal. The plot of Legends will give you migraines if you think about it too much.
Jake's death, and the subsequently epic time-and-space-altering events that bring him back from the dead in The Dark Tower.
The book Starbright and the Dream Eater has one, after Starbright manages to defeat the Dream Eater. She wakes up the next day and finds that every single reference to the "spindle sickness" that the Dream Eater created is instead replaced with a reference to a dangerous pesticide. Every person who got sick from spindle sickness got sick from the pesticide instead, and no-one except her remembers the Dream Eater even existed.
Averted in the Star Wars Expanded Universe. Jacen Solo's brother, Anakin, died. Jacen developes the power to use the Force to time travel. Jacen's Sith apprentice is Anakin's girlfriend. Jacen's time travel, however, can only alter the events in his memory, not in reality.
Apparently, bringing Anakin back from the dead was seriously considered for the ending of Legacy of the Force, but they figured that messing with time travel in the Star Wars universe could be pretty messy.
Used in the Star Trek: String Theory novels. When Voyager accidentally meddles with the "strings" underlying reality, space starts to unravel. The solution to the entire mess eventually involves rewriting thousands of years of history. An event which actually occurred within the current story (all photons within a certain range being drawn into Exosia, a realm of subspace) is now placed many millennia in the past. The starless Void from the Star Trek: Voyager Season Five opening episode is the result of this event. Its existence is therefore one big Cosmic Retcon, down to the species who developed there but technically didn't exist until a few weeks prior...
And in the spinoff series Angel, the title character makes a Faustian bargain to have his son retconned into having lived a happier childhood and not remembering his real life (in which he was raised by a psychopath in hell). As a consequence, everyone else forgot about the boy's existence; so in a sense, it's the exact opposite of the Dawn scenario. CW higher-ups requested the retcon due to the show's dense continuity, which ended up being dumped back into the plot anyway.
The latter part of LOST season 5 concerns the main characters, having traveled to 1977, attempting to prevent the plane crash which initially brought them to the island, thus undoing everything that has happened so far in the series. It doesn't work, though it does create its own side-effects later on.
In series 5, the cracks in the universe play a similar role, erasing Rory Williams and the Doctor from history. They got better.
The Doctor Who Expanded Universe has a far more insidious form of this with Faction Paradox's Paradox Biodata Virus. It latches into the part of your biology linked to the Time Vortex... and makes it so you always have worked for them and always will. The Eighth Doctor was infected, and his timeline nearly destroyed.
The Ancestor Cell, based mainly around said Faction, features a huge and weird one with the Doctor's destroyed TARDIS retconning it back, after holding both timelines intact for quite some time, and blasting the sector of space that included Gallifrey into quarks.
In The Name of the Doctor, the Doctor's open timestream at his grave on Trenzalore provides The Great Intelligence with an opportunity to successfully retcon the Doctor's entire timeline, and Clara has to intervene throughout the Doctor's history to retcon the retcon. However, as of The Day of the Doctor, the Doctor no longer dies on Trenzalore, so the retcons may never have happened.
In the 50th anniversary special Gallifrey's destruction itself is retconned. Instead of destroying it, the Doctors sealed Gallifrey away in a pocket dimension, and Eleven then goes looking for it.
In Big Finish Doctor Who, Charlotte Pollard being saved by the Doctor causes her to become a living paradox meaning history starts breaking down, the CIA are around in 1937 before they should have been formed and Benjamin Franklin was a President. However after she saves the Web of Time the paradox and these events become part of the Web therefore there is no paradox. Timey-Wimey Ball indeed.
Occurs near the end of Mighty Morphin' Power Rangers. The villains turn back time to a period a decade or so before, and when the effect was canceled, anything that had changed during the reverse-time led to changes in the present day. Most notably, Aisha had moved to a small African village as a child, and Tanya's Adventurer Archaeologist parents had left her in America rather than the African village.
Balthazar attempts this in Supernatural, traveling back in time to save the Titanic: this has the effect of ruining Celine Dion's career, creating 50,000 new souls for Castiel, and preventing the deaths of Ellen and Jo Harvelle. Unfortunately for them, Castiel resinks it at the end of the episode.
Though only because Fate called him out on it - the whole thing was on Castiel's orders, in order to create new souls for the civil war in Heaven that he's losing.
The fourth season of Fringe picks up in a timeline that's been cosmically retconned as a result of Peter being erased from existance at the end of season 3. The differences are subtle — the prime universe Fringe Division has a different lineup, Walter is a shut-in, some characters are now strangers — but most of what happened in the previous seasons seems to have unfolded in the same way, or at least similarly.
Kaizoku Sentai Gokaiger has the power of the Greatest Treasure of the Universe, which lets its discoverer rewrite the universe to suit their own desires. The Gokaiger ask if it could eliminate Zangyack, and are told that it would be as if Zangyack never existed — but that they would also erase all of the Super Sentai from existence too. They end up rejecting the "wish", deciding to take on Zangyack themselves, because facing impossible odds is what Super Sentai members do, and because they don't want to lose everything that they've gained and become as a result of the hardships Zangyack inflicted upon their lives.
Nobilis has one of these in its Back Story. Something like 500 years of time were erased, but in an uneven way so that some events moved back the full five hundred years, some a portion of that and some not at all. The souls of all the people on the space colonies this erased are very upset, and seemingly still on the planet they used to live.
This is also the goal of the Excrucians; they attack aspects of reality, causing them never to have existed.
In GURPS Infinite Worlds, a retcon is called an "ontoclysm" or "reality quake", described as a cosmic event that can change the past and even the natural laws of a given universe. The game even gives rules for attempting to trigger one! It has been mentioned that superhero worlds are especially susceptible to reality quakes, and that any world with magic or super-powers could be explained by "shards" of the previous reality existing in the new universe (which sounds much like the DCU's explanations about the various Crisis of Infinite Retcons).
One of the last adventures for Dungeons & Dragons 2nd Edition was Die Vecna Die!, in which the titular evil god gains control of the city of Sigil, a Cosmic Keystone that lets him restructure The Multiverse to his whim. He fails, but the city's rightful ruler, the Lady of Pain, can't put everything back together perfectly. This was implicitly meant to explain away the differences between the cosmologies of 2nd and 3rd Editions.
Exalted manages to have its own equivalent of Crisis on Infinite Worlds during a First Age Historical Event called "The Time of Cascading Years". It was a rare foray into Temporal Mechanics for the series; Creation had split into 700 separate timelines, each one with only a single Celestial Exaltation in it. The timelines each reintegrated when that timeline's Exalt managed to save Creation in some massive way... which took longer for some than others. First Age historians basically ended up hand waving the calendar as 'skipping over' the Time of the Cascading Years in the year count, as some timelines were hundreds or thousands of years older than others. The writers primarily introduced it to allow Player Characters in the First Age to have Multiple Conflicting Continuities about "Who saved what from whom with how many chickens", who got to wield the Aidenweiss, and other sorts of badassery that would otherwise be exclusive to historical NPCs.
The Mage: The AwakeningSourcebookImperial Mysteries introduced this as a big trick of archmasters. Via Imperium Rites, they can build off of changes they've already made in the world to alter fundamental truths of reality, retroactively introducing changes to history or cosmology. This is part of how one becomes an archmaster (rendering the facts of one's existence only vaguely remembered to mages and not at all to others), and is the most well understood path to Ascension; you remake the world into one where your transcendence is and always was a fundamental property. Ripple-Effect-Proof Memory is possible, but only to archmasters and only while within their Golden Road.
The game Time Hollow involves the main character "fixing" Cosmic Retcons caused by the game's villain.
Sonic the Hedgehog (2006), in which the ending writes the game out of continuity, though Sonic still has memories of what happened.
And then Sonic Generations happened, reintroducing the game as an alternate timeline.
City of Heroes has the PsychoChronoMetron, a device that allows psychics to alter the world. It was only used once; as something of an aversion, it caused a Continuity Snarl as the villainous inventor attempts to use it to turn a hero into an ally, without knowing anything about his history. The history of this hero was left... somewhat confused.
This happens in Suikoden Tierkreis whenever the world undergoes a radical change. The cause of these events is worlds fusing together, the actual retcon part is an effect of the True Chronicle.
The newest Mortal Kombat game has the Raiden from Armageddon broadcasting a premonition to himself around the time of the tournament from the first game. The Raiden of the past is now imbued with knowledge of events to come and sets about changing them (hopefully for the better).
Failure, thy name is 'Raiden'. Through the inscrutable phrase "he must win", Raiden ends up making things a lot WORSE this time around. By the end of Mortal Kombat 3, his misinterpretation of said phrase leads to nearly every single Earthrealm warrior dead and just in time for the events of Mortal Kombat 4 to begin with a massively stacked deck for the side of evil. It's still a Cosmic Retcon as he averted the Armageddon and possibly sealed Shao Kahn for good...but at a terrible cost.
In Fable II, Lord Lucien originally intended to rebuild the Tattered Spire in order to bring back his deceased wife and daughter, but by the time the Hero of Bowerstone gets to him to rescue the other three Heroes who are trapped by him, Lucien decided that the world itself needed a Cosmic Retcon. However, the Hero of Bowerstone prevents Lucien from accomplishing this and either kills him or lets Reaver shoot him after explaining himself. After this, Theresa gives the Hero the choice of one of three wishes, two of which are in themselves retcons of history.
In Mega Man X 6, Capcom retconned Zero's Death in X5, shoehorning him into the plot (if you found and defeated a Nightmare Zero).
The events of the first game of the Prince of Persia: The Sands of Time trilogy are retconned twice. First within the game itself, when the Prince rewinds time at the end of the game and kills the Vizier that kicked off the events of the game, and then again at the end of Warrior Within, inadvertently retconning the Vizier's death, causing him to come back as the Big Bad of Two Thrones. By the time Two Thrones rolls around, the first game's story has ceased to exist in its entirety, and only the Prince remembers what happened.
Final Fantasy Crystal Chronicles: Ring of Fates has this as its ending. The Yuris and Chelinkas from every parallel world rewrite reality to prevent the tragic events of the game and resurrect their family. Yuri and Chelinka remember, but nobody else does.
In Narbonic, Dave goes on a time-travel adventure. Afterward:
Dave: I guess this proves that time is a closed system, unalterable, our fates inescapable. I guess I'll have a cigarette and brood.
The original run of Zortic ended with a fight between two cosmic beings creating a big swirly Negative Space Wedgie, which the heroes all fell into. The comic went on hiatus for a short time, and then came back, starting over from the beginning. The original run of Zortic was based exclusively on parodying popular science fiction franchises; the two cosmic beings were arguing over the merit of this. The new version is intended to be more original and less parody-driven.
Fairly late into Homestuck, John and an entourage of trolls find a supposed weapon that could be used to destroy the Big Bad. It is intangible, however, and reaching into it causes John's arm to show up all over the comic's history. To help sell the effect, the panels in question (and a few Flash animations) had the arms put in retroactively.
An explicit power of the Big Bad in Captain SNES: The Game Masta. So far, it seems she can only retcon things within the framework of existing backstory, fleshing things out in a way favorable to her... but its implied that at full power, she isn't so restricted.
The non-canon El Goonish Shive, EGS:NP storyline "Oblivious Wand Waving" features a wand that does this while seeming to do nothing from the perspective of both the user and everyone else around them.
In Worm, part of the author's justification for his rewriting of Chapter 7.9 a day after it was posted was Coil, the boss of the protagonist's team, had the power to split the world into two timelines and then collapse whichever one he didn't like.
In season 2 of Danny Phantom, Danny accidentally gets his ghost powers removed by a Literal Genie, leaving Sam to recreate the event that gave him his powers in the first place, except she puts a "DP" logo on his suit so that he'll have it in ghost form. When she decides it'd be easier to just wish everything back to how it was, she does so, but specifies that the second version of him getting his powers be the canon one, because she really likes how he looks with that logo.
Fry's travel back in time created his time-copy, which also allowed to retcon the most heartbreaking episode of the series.
In fact, the whole Bender's Big Score movie is just made of this trope. It even leads to a giant rip in the universe by the end when Bender meets all of his past selves hidden in the caves under Planet Express with all of history's treasures and convinces them to all emerge at the same time instead of when they were supposed to, at which point Nibbler exclaims "Everyone out of the Universe!" and eats himself.
All the retcons in Ben 10: Omniverse are explained by the entire universe getting destroyed and then getting imperfectly recreated by Ben in Alien X form in the seventh note technically fourth episode of the series. One of the main changes is that the living planet Primus, which used to be a massive DNA storage for the Omnitrix and which played a major role in season 3 of Alien Force, no longer exists. Whether this means Eunice is also Ret Gone is unclear; she was on Primus, but her existence wasn't directly tied to it. Word of God is that she's "unlikely" to appear in Omniverse.
Scooby-Doo! Mystery Incorporatedends with one. The Nibiru Entity is defeated when the crystal sarcophagus it was using to draw power from another dimension is destroyed. This results in the sarcophagus imploding into a black hole and erasing the Entity from existence. As a result, everything is changed to be as if it never existed at all.