Commonly abbreviated AU, stories of this type are usually what-ifs, where possibilities arising from different circumstances or character decisions are explored. Unlike regular fan fiction, which generally remains within the boundaries of the canon set out by the author, alternative universe fiction writers like to explore the possibilities of pivotal changes made to characters' history, motivations or environment.
The author also gets a built-in audience, the fans of the altered universe, for their story, which they would not get if they wrote it as an original story instead of fan fiction. Some of the best fan fiction writers who aspire to be published authors can take advantage of this in the opposite direction by having a built-in audience, the readers of their fan fiction, for books they might publish.
An example of this is the Daria fan fiction, "The Art of Seeing, which explores what might be different if Jane were blind.
Stories in this category of AU follow the established canon before veering away at a crucial moment (similar in concept to many entries in Marvel Comics' What If series). An example of this is "A Moth to the Fire, by Sera dy Relandrant, in which Ariana Dumbledore does not go out to play on the day she is attacked by muggle children in canon, and thus does not lose control of her magic, altering the life of her brother, Albus Dumbledore, and eventually the entire world.
Some alternate timeline stories are called "denial-fics" because they ignore certain events in canon. For example, many Harry Potter denial-fics pretend Sirius Black never died. An example is "You Don't Belong Here" by Hieirulesall; the author's notes say that the author wants Sirius alive but does not want to find a way to bring him back. Others are called "fix-it fics," because they rewrite the story so that the events in question did happen, but the fan fiction undoes the consequences. An example of this is "Extenuating Circumstances" by SarahtheBardess, in which Sirius Black is returned to life.
These stories take the characters from a series and place them in another time, place, or situation. An example is "Simple and Clean" by Ethelfraed, a Yu-Gi-Oh! story that transfers the characters to Normandy in 1066. A subset of this type, called familiar contextual reassignment, takes the characters from a series and places them in a setting more familiar to the author. This type of context shift is one of the main sources of "high school fic," in which all the characters are written going to high school. An example of this is the Charmed fan fiction "Charmingly High School" by AlwayWrittinSomethin, in which characters who never met until adulthood attend high school together.
The actors may find themselves in the fictional universe, the fictional characters may find themselves in the "real" universe, or the story may feature both sides of the swap. This type of AU has appeared in mainstream publication as well, in Star Trek short stories from the early 1970s in which the actors from the Desilu set were swapped with the "real life" Starfleet officers via the transporter. ("Visit To A Weird Planet "Visit To A Weird Planet, Revisited). These fan fiction stories were eventually published in official Star Trek books. This trope has been used in other places, such as the film Galaxy Quest.
Two fictional universes, or the real universe and a fictional universe, are placed in a situation in which they interact. Such stories sometimes involve comparisons and conflict between the combat prowess of the two universes, often involving the various strengths and weaknesses of the technology/magic of each world. An example is "A Thin Veneer" by AlbertG, in which Star Trek characters meet Babylon 5 characters, setting off a galaxy-wide war. Sometimes these stories involve characters from one universe substituting for the characters in another universe and playing out the second universe's storyline, as in "Return of the Aurors" by Anne Walsh. The fan fiction recasts Return of the Jedi with Harry Potter characters, like 'Ron Solo', Ron Weasley as Han Solo, and 'N-3LO', Neville Longbottom as C-3PO. The story is played out in a Harry Potter-themed universe, visiting, for example, Dursley the Hutt's home on the desert planet of Quidditchine.
Alternative universes can arise inadvertently in fan fiction when the source material is released in a serial form, such as a multi-season television series or a book series, so that fan works are written before further canon arrives. For instance, much Harry Potter fan fiction in the nearly three years between the publication of Harry Potter and the Goblet of Fire and Harry Potter and the Order of the Phoenix was written as "continuation" fan fiction, but became AU as soon as the new canonical material appeared. An example is Arabella and Zsenya's "After the End", made AU by Order of the Phoenix the day after the story's completion. In "After the End", Harry's fifth year ended with Albus Dumbledore's death, which did not happen in Order of the Phoenix.
On occasions, a fan fiction writer will create a character that is supposed to be there from the beginning and does not exist in the actual story that inspired it. Gertrude 'Danger' Granger in Anne Walsh's Harry Potter AU series, the "Dangerverse," is an example of this. It is also not uncommon for fan fiction to deliberately explore what could have happened in the original fictional universe had certain events played out differently. Changing canon can also mean taking a canon couple that was hinted at, but didn't actually happen, and expanding on it (for example some elaborating on Soi Fon's obsession with Yoriuchi in the manga Bleach).
Many fan fiction readers and authors dislike AUs because some AU writers disregard the canon of official work by or approved of by the author. However, some authors specifically write AU fiction instead of textbook fan fiction in order to explore issues which were not fully addressed in canon, and may present a meticulously researched canon universe which then veers away from actual events in ways which logically proceed from the changes the AU author introduced.
Another type of AU that authors and readers have problems with involves the storyline of a well-known movie or video game, played out by original characters or by characters from another series. An example is "A Different Sort of Adventure" by ImLucky, in which original characters work through two of the Pokémon game adventures. Finally, some people have theorized that because AU authors are already radically changing the story as it is, they find it far easier to add a Mary Sue wish-fulfillment character.
A common mistake made by inexperienced fan fiction writers is to believe that writing an AU fan fiction means that the writer can acceptably and drastically alter the personalities of major characters; in fact, the point of AU fan fiction is that the characters' personalities remain as much the same as possible, and the only changes are those which would rationally be caused by the differences from canon.
In the many Gundam anime series, there are six major timelines that are independent of one another, and some fan circles (especially in North America) refer to the timelines created after the original Universal Century as "alternate universes." However, this does not truly fit the standard definition of AU, as the timelines share neither characters nor locations (aside from the solar system itself). Tenchi Muyo! and El-Hazard utilize the more traditional alternative universe concept, each beginning with an OVA series and followed by a TV series that utilizes many of the same characters and locations, but with alterations made to both (some minor and some drastic).
The Star Wars: Infinities comic book series explores alternate universe fiction in a "what if" style, diverging from the story of the original Star Wars trilogy movies at crucial moments, with a major impact on the evolving story.
Marvel Comics publishes many alternate universe stories In addition the Stargate franchise has included episodes in which characters interact with alternate versions of themselves.