Co-op Mode: Of a kind wherein James exists since birth in the Wormverse. A closer example could be that Gaia exists, and thus is at work with helping parahumans (like Contessa/Fortuna) in defeating Scion.
Always Advancing is a Girls und Panzer fic where Yukari Akiyami mysteriously finds herself waking up to six months before after the events of Girls Und Panzer, and that she is transferring to Saunders University High School, Oorai apparently having shut down and the remaining student body moved to other school ships.
Batman Beyond Revisited has Bruce Wayne die in his final battle with The Joker, and Terry McGinnis is replaced with an OC, runaway Jake Vance, who is recruited by the inheritors of Wayne Manor, Dick Grayson and the Oracle Barbara Gordon.
Child of the Storm has the basic premise of Thor having been incarnated as James Potter first time round on the humility thing. This went about as well you'd expect, with the trauma of being violently murdered, then watching helplessly as his wife was murdered driving him nuts, necessitating a mind wipe and a return to square one. Also, Lily turns out to have been first cousin once removed of Jean Grey and accidentally called upon the Phoenix to protect Harry - which explains the incendiary component of the protection - and is not exactly dead, as such, which, needless to say, changes everything. It grows into a massive Inter Continuity Crossover, sticking the Marvel Cinematic Universe, Harry Potter, The Dresden Files, and Smallville in a blender and is spliced with elements of Marvel Comics,DC Comics, and Merlin (2008) to create something entirely different. There's even a few sly references to Good Omens.
Evangelion 303: In this alternate world Second Impact did not happen, Seele is a terrorist organization and does not plan an Assimilation Plot, there are no giant robots or alien monsters, the Children are in their twenties and pilot war planes, Kaworu is a human being, apparently Rei is unrelated to Shinji...
Supergirl fanfic Hellsister Trilogy is reality similar to the Earth-One universe which was born when the Anti-Monitor was defeated early on.
HERZ: In this story Third Impact never happened. The divergence was created when Rei felt Shinji's despair at being unable to save Asuka. Rather merging with Lilith's body, she absorbed it and flew to help him, shattering the bakelyte encasing Shinji's mecha. Both hurried to help Asuka and managed to save her just in time. Twelve years later Misato leads an organization tasked with preventing the proliferation of Evangelion technology, Shinji and Asuka are married and raising their child and SEELE is still plotting The End of the World as We Know It.
Charlotte Flair is a crime boss, the head of one of the most powerful crime families in the country.
Becky Lynch is a soldier with the Vegas Irish, a lower level criminal organization.
Bayley Martinez is vice detective with the Las Vegas PD.
Sasha Banks is a nurse at the local hospital, and Bayley's girlfriend.
iSwear, an iCarly fanfic, starts with Carly entering an alternate universe, and every time she loses consciousness she is automatically evicted from one universe and pushed onto another in a manner similar to Quantum Leap and Sliders. The horror kicks in when you find out that other versions of Carly have been doing the same thing and that many have died due to ending up in dangerous Crapsack Worlds.
Just One, Big, Happy Kingdom is a Merlin fanfic in which an eighty-year-old Merlin decides to teach his younger self a lesson by putting him in a mirror universe ("Not-Camelot") and put Not-Merlin in the normal Camelot. It's one of those mirror everybody-is-his-opposite universes.
Mass Effect: Clash of Civilizations: Aside from the obvious (the UNSC in place of the Systems Alliance, the Covenant species existing, the whole Halo side of the crossover), in this universe the Council lifted the ban on opening closed relays several years before the start of the story. In canon Mass Effect, this never happened, and even during the trilogy the law against opening relays was still upheld. In addition, the Reapers were created by the Precursors to eradicate any race that seemed to threaten their galactic primacy and were later ordered to leave the Perseus arm alone, leading to the rise of the Forerunners and the ancient human empire, while the asari are a literal Human Subspecies created by the ancient humans and seeded halfway across the galaxy in a last-ditch attempt to survive the Forerunners' genocide in some form.
Also, Starfleet Humans takes place in the same alternate universe that Equestria Girls took place in. However, Mykan is on record as saying that it is an alternate continuity that takes place near the end of MLP's 3rd Season.
The Odyssey, an Exalted fanfic. It's notable for both its quality and the fact that the point of divergence has not yet become apparent. Something happened to the Fivescore Fellowship, though..
Two of these exist in Phoenix's SSBB Case Files, named Alternate Turnabout and Alternate Turnabout 2. The first has Larry Butz working as a defense attorney, with Adrian Andrews at his side, while 2 features Franziska von Karma and assistant Dick Gumshoe working for the Wright and Co. Law Office.
The Pony POV Series has such a thing. It's explained that all the worlds diverged from the Heart World (implied to be the actual shows' timeline) and are effected by changes there, but can break off and continue on their own in the event the change in the Heart World is so great said universe can no longer harbor the connection. The ones the series itself focuses on are its main timeline and the Discorded Timeline, a Villain World ruled by Discord, but we also see a lot of alternate timelines which Princess Luna refers to as "possibilities and impossibilities". Applejack gets to see quite a few of them on two separate occasions, the one that means the most to her being the Orangejack universe, where she never left Manehatten. She eventually gets to meet Orangejack and they team up to fight Nightmare Mirror, Applejack's own Superpowered Evil Side who may or may not be another alternate version of her. It also turns out Orangejack is an Element Of Generosity and there are universes were Applejack was one of the other Elements as well, all of which are summoned to fight Nightmare Mirror. There's also a universe were Rainbow Dash turned into Nightmare Manacle, another where Pinkie Pie turned into Nightmare Granfalloon, and another were the mane cast are the Mighty Morphing Power Ponies fighting a Goldar version of Gilda. Oh and Pinkie Pie is actually the G3.5 Pinkie Pie and is how she is thanks to being left pretty much untouched by a Cosmic Retcon that turned that universe into the G4 universe.
Reality Is Fluid starts out with the USS Bajor being tasked with testing a new sensor array designed to detect and observe alternate universes. Two of the universes detected are an AU where the Federation apparently lost the Dominion War, and the Star Trek Novel Verse (the fic is based in the Star Trek Online timeline).
Riding the Dragon diverts the BattleTech universe by having political intrigue change the course of House Kurita in the early 31st century.
Scarred Survivors is a retelling of the Ah! My Goddess manga. A wish has enslaved Belldandy to a depraved pedophile. Urd enlists the help of a soldier in order to save her, a Navy SEAL by the name of Keiichi Morisato.
The Son of the Emperor mixes the real world with the world of My Little Pony: Friendship Is Magic. This results in an Alternate Universe where the ponies grow to the size of horses and have been used for centuries in warfare, mytical creatures like griffons are commonplace and magic exists.
Streets of Rage Saga, a 10-story saga based on the Streets of Rage game series (both the canon trilogy and several fan-made games and remakes based on said trilogy), takes place in a setting based on but highly different from the canon. Just a few brief examples, with the canon information in parentheses: Axel lost his father in a fire that was set by the man who would later become The Dragon for the first story's Big Bad (in canon, no mention is made of Axel's family members); Blaze comes from a Doomed Hometown that was razed by The Syndicate (in canon, the only back-story on her is that she was a rookie cop who quit alongside Axel and Adam because of the force's corruption); and Mr. X is a U.S. senator with the full name of George Xetheus (in canon, his real name wasn't divulged and his role as a Corrupt Corporate Executive was only hinted at in canon and expounded on in Bombergames' remake).
The Uplifted series does this, by showing what happens when Humanity is uplifted circa 1942 by the desperate Quarians with the intention of using them to retake Rannoch.
With Strings Attached is set on another planet in an alternate universe. Additionally, the four visit three other universes (including one set in a 1950s New York, more or less); the Fans are watching from their universe; the Dalns gods inhabit yet another universe; and Jeft comes from still another.
This trope is likely to be used by anyIntercontinuity Crossover fanfic in which the melded continuities would otherwise contradict one another.
An ER fanfiction series titled "Dreams That You Dare To Dream" had several of the main characters leaping to alternate universes in which several of the show's major changes never took place—Carol did die from her suicide attempt from the first episode, Susan Lewis never left town and married Mark Greene, etc. Another one set on New Year's Eve 1999, titled "Countdown", took a similar form, though it only focused on the typically unpopular Kerry Weaver.
Sonic X: Dark Chaos is this to Sonic X, thanks to a few points of divergence in the back story of Sonic X Season 3. The biggest change is that Cosmo's race was destroyed by their own creations rather than by the Metarex. This ultimately causes several more outside factions to get involved in the Metarex arc, with very bad consequences for the galaxy.
It's never been clear whether the Supernatural episode "The End" took place in the actual future, an alternate timeline, or a construct designed to be as distressing to Dean as possible. Down to Agincourt takes the view that the timeline really exists, and now that Dean's time has "caught up" (mostly, we think), it's more of an alternate universe than a Bad Future.
Total Shuffled Island Series is this to Total Drama. Every contestant that has competed in the first season all the way up to the sixth has had their introductory season changed around, leading to a different run of events such as different teams winning a challenge or different couples forming.
Underswap, where the main character pairs switch places in terms of personality. Toriel is the Queen hunting down humans while King Asgore treats the player like a surrogate child; Papyrus is a lazy slacker while Sans is an excitable sentry; Alphys is head of the Royal Guard while Undyne is a bookish scientist; Mettaton is a melancholic snail-farmer while Napstablook is the Underground's celebrity, and Flowey is usually swapped with Temmie.
Mafiatale, where the monsters are a gang operating out of 1930s America.
Outertale, where the monsters were exiled to a far-off planet and the player is an astronaut.
The Thought, which explores what might have happened if Sans killed the player as soon as they left the Ruins.
The Error Universe, created from a copy of the game that was mangled beyond recognition and which spawned Error Sans, who wants to end the Multiverse entirely.
HELP_Tale, a universe populated entirely by horrorsformed from the amalgamated bodies of every version of a character in the multiverse, jammed together.
Baby Blasters, an off shoot of the Gasterblaster AU where young Sans and Papyrus can change shape to resemble the Gasterblaster weapons, with the flagship fanfic being Trust, as well as a thriving Tumblr Community.
There are apparently two universes the stories take place in; the main one, and a second world where Paul takes more actions that could be termed renegade, such as turning Sportsmaster into a construct, trying to steal tech from the New Gods, injecting himself with Venom Buster, and eventually begins calling himself Grayven.
And there is the Crime Syndicate universe, aka Earth-14, which take place before and after the events of Justice League: Crisis on Two Earths. Here, Paul is a Blue Lantern, who goes by the name of Power Ring and is a Made Man of Ultraman, and is technically babysitting the more adolescent tempered Young Offenders in check.
The Fool's Canon arc brings into picture of other alternate Pauls with different power rings in the wider multiverse.
An Anti-Green Lantern Paul, who is a reluctant villain that is being controlled by his power ring, in a version of the DCAU in which it includes Cyborg being a founding member of the Justice League and a abundance of sidekicks closely participating in the League.
A Red Lantern Paul exists in the regular Teen Titans universe.
An Indigo Lantern Paul who is in The Boys universe.
There are several in the Sgt. FrogYin And Yang Series, both made by the author herself and by fans of the fic. It helps that several major characters are reality-warpers.
crawlersout: Odd case. Fem!Harry's house is connected to two separate universes: one is set in her original time, years after the defeat of Voldemort, where the plot of the original Harry Potter series happened (just with Harry as a girl). The other is an alternate universe set in the 1930s, where the point of divergence is Harry taking in a young Tom Riddle Jr. a few years before he is set to go to Hogwarts. The main plot occurs in the latter setting, where Harry is raising Tom and interacting with some of the most prominent figures in this era (more specifically, Gellert Grindelwald, with Albus Dumbledore slated to appear later), with occasional dips into the former setting.
Constants and Variables: With Elizabeth in control of her abilities and accidentally passing on some of her quantum powers to Harry, alternate worlds are brought up and presented in the story.
For Christmas break, Elizabeth takes Harry to an alternate version of Rapture, a world where Plasmids and Fontaine and all of the factors that led to the canon-Raptures demise never happened and the city has been thriving up to present day.
After finding out that Narcissa drugged her tea with veritaserum, Elizabeth decided that showing Narcissa the result of her and her familys loyalties, taking them both into a world where Voldemort won and rules supreme. Not much is shown, the only things they could see being Hogsmeade (now nothing but ashes) and a mass graveyard where the Shrieking Shack used to be. The graveyard was dug by neutrals and were used to bury the failed La Résistance while the neutrals where killed and thrown in a ditch when Voldemort and his followers inevitably turned on them.
When Elizabeth and Harry learn about the Philosophers stone, they venture into an alternate universe where the first year has not commenced yet, sneaking into the corridor where the stone is meant to be hid in before all of the obstacles and traps are laid out. When the Dumbledore of that universe finds them, he mentions that he is expecting the Girl-Who-Lived to be introduced to the school, that universes version of Harry being female.
After spending the minimum month with the Dursleys, Elizabeth takes Harry to an alternate New York within The Purge universe.
Izuku lives in a universe where Quirks are common and Spider-Man is fictional. He's bitten by a genetically-altered spider and becomes Spider-Man instead of obtaining One For All. Peter lives in one of the many versions of the Marvel Universe and ends up dropping into Izuku's universe after a fight with Mysterio.
A sidestory, "The Tangled Web of Spider-Woman", has a universe much like that of the original My Hero Academia, except organizations like Os Corp exist and Melissa Shield is one who gets bitten by a radioactive spider, becoming spider-Woman.
To Hell and Back (Arrowverse) is a League of Assasins!AU with Oliver, Barry, and Kara. National City and most of Supergirl (2015)'s supporting cast doesn't exist in this reality; Kara instead bases herself out of Starling City, along with Oliver.
Alternate History is an Avatar The Last Airbender comic where Aang broke out of the iceberg twenty years later than in the cartoon.
Hatchling Quest: Earth Bet is this to Samus home dimension. It turns out that the setting is this to canon Worm even before Samus showed up.
Marvel Crossroads is a shared continuity group that takes place in an alternate marvel timeline, diverging after The Galactus Trilogy (Fantastic Four #48-50).
From the Ashes is a Fullmetal Alchemist fanvid where Edward wasn't able to transmute Al's soul into armor. He's on a quest to find a Philosopher's Stone and revive Alphonse.
Son of the Sannin features an universe where Jiraiya and Tsunade become Naruto's legal guardians, and stay in Konoha to raise him during his childhood years. The ripples in time result in many changes from the original story, ranging from minor ones such as Jiraiya and Tsunade getting married and Naruto getting close to Hinata much earlier, to major ones such as the Uchiha Clan actually carrying out their planned rebellion and the aftermath resulting in Konoha having to up their academy standards to make their new generation much stronger to face future threats.
The Hounds of Vegas takes place in a WWE AU where the members of the Shield are cops. In addition, it was inspired by The Horsewomen of Las Vegas.
Us and Them: Vincent is awoken twenty-two years earlier than in Final Fantasy VII, goes and breaks Sephiroth out and leaves him with Aeris' family. Divergences from canon proceed.
The DC Universe/RWBY fanfic Hunters of Justice features this for both series. The depiction of the DC universe is a Patchwork Fic whereas the RWBY section, while featuring elements of stuff that came since, deviates from canon with Brainiac crashing the Vytal Festival before Cinder could enact her plan, thus featuring a version of Yang still with her right arm, a still-living Pyrrha, and Ozma still in his Ozpin form. That said, even putting the non-canon Elseworld chapters, it is partly a DC fanfic, so the Multiverse comes into play and it's discovered by Batman that there's some versions where Yang losing her arm and Pyrrha dying still happened.
Eight Count is a Batman AU where many Gotham-associated characters are involved in boxing, whether as fighters, trainers, promoters, managers, etc.
A series of JoJo's Bizarre Adventure named "Jojo's Bizarre Adventure: A New Universe" by mtnetwarrior is set in... well, a new universe. The main point of divergence is the presence in each part of Stand-wielding human versions of one of the Mane Six or allies or the Princesses. Other notable divergences include:
Jotaro Kujo's father, Sadao Kujo (who is reimagined as a Stand user) participates on behalf of car business CEO Valentine in a cross-country motorcycle race acting as this fanfic's version of the Steel Ball Run from Steel Ball Run, reimagined as a motorcycle race. Also, it takes place before Stardust Crusaders.
Alternate versions of characters from Steel Ball Run and Jojolion, the characters from the former adventuring in an alternate version of Overlord with plenty of Stand Users and the characters from the latter very intertwined with the universe's version of Danganronpa.
Most importantly, the alteration to the universe by Pucci is not allowed to last in the fanfic's version of Stone Ocean.
A fanfic named "Heroes of Remnant"  which is a crossover between RWBY and Persona 5: namely, the fact that Personas are wielded by RWBY characters. Also includes reimagined non-Animatronic versions of characters from Five Nights at Freddy's ("A Reward Long Overdue" by Salvador Tepes , a crossover between Five Nights at Freddy's and RWBY, being the foundation for their inclusion).
Spawned its own version of RWBY Chibi called "Everyday RWBY" .