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- In The Movie of the first anime, it's shown that everyone in Amestris has an Identical Stranger living in our world, which is on the other side of the Gate. Since only a small handful of characters have their alters depicted in-canon, anyone else is up for grabs for fanfiction writers - and this includes some pretty popular characters who get frequently shipped with the protagonists, like Winry Rockbell and Roy Mustang. Having Ed and/or Al run into and possibly date their alters is a common fanfiction trope. It's not uncommon for writers to play with the historical setting, like by making Alter Winry/Roy/whomever a Jewish person and the characters needing to get out of Germany before it's too late, etc.
- More than a few fics ignore Alfons' death and have him living alongside Edward and Alphonse. Noah mysteriously gets ignored in many of these.
- "Winry or Roy crosses the gates and gets reunited with Edward and Alphonse" and "The Elrics cross back to their world" fics are a dime a dozen. On a more pessimistic note there are the "Winry/Roy angst about Edward" fics where they have to learn to live without him. Or even worse, not.
- The fact that homunculi are the results of failed human transmutation leads to a lot of "well what if someone tried to resurrect this dead person, and meets their homunculus?" Particularly common with Roy Mustang and Maes Hughes, especially if it's a ship fic.
Manga and Brotherhood
- What happens when Pride grows up all over again? What if he gets his memories back? What if he doesn't but regains the shadows? What if he gets the shadows and then the memories?
- The most common Fix Fic here is usually to have Ed gain back his alchemy. It's essentially the Mangahood side of the fandom's version of "bring Ed and Al back across the Gate."
- Interestingly, there's also a common reverse-Fix Fic in "keep Roy Mustang blind," because many fans thought having the stone magically cure him cheapens the story's message or his character arc. Or they think the trope is ableist. Or they just want to make his get-together with Riza, Ed, Havoc, Olivier, etc. extra angsty.
- People who ship Ed with someone other than Winry often attempt "canon compliant" fanfiction that explains how they split up after the ending, which shows them married with kids. These can unfortunately devolve into Winry-bashing, but increasingly fans are more interested in making it more mutual, often giving Winry a love interest of her own (usually Alphonse or another female character).
- Fics where the anime characters meet their manga counterparts, or they get transferred to each other's universes, are written. One increasingly common version of this involves Crack Ship fics of Canon Foreigners from opposite canons. For example, Tierfal, a popular slash writer in the fandom, has written several fics that ship Alfons Heiderich (the Alter!Al who lives with Ed in Munich in the 2003 anime sequel film) and Major Miles (one of the Briggs soldiers who only appears in the manga/Brotherhood).
- Role reversal fanworks where Edward is the soul bound to the armor and Alphonse has the automail arm and leg are pretty common.
- State Alchemist OCs who were Self Inserts used to be so common they inspired compilation websites and parody fics.
- An even weirder thing people used to do a lot was come up with a new homunculus. Since the homunculi were based around the Seven Deadly Sins, the writer had to come up with a new sin to add to the list. Some of these could be pretty laughable, like "unpatriotism."
- It's not uncommon to read post-canon fics that are completely canon-compliant, except that one or more major character deaths never happened. (How the story managed to reach the same endgame without such crucial turning points is anyone's guess.) The most common candidate for this kind of resurrection is Hughes, especially in anything where Roy Mustang is a central character and needs a mentor friend who isn't Riza. Greed is also a common resurrection candidate, particularly for fics involving Ling.
- Roy/Hughes shippers usually accept Hughes' love for his family as a crucial part of his character, and go to great lengths to write their fics in a way that avoids having him break up with or cheat on Gracia. This usually involves consensual polyamory, making Roy's feelings one-sided, or setting it before Hughes meets her/in an Alternate Universe where she doesn't exist.
- Fan-works where Roy and Riza are in a Secret Relationship together.
- Depicting the Elric brothers as Ishvalan or half-Ishvalan.
- In AUs where both Hughes and Nina live, it's pretty much the norm for the latter to be Happily Adopted by the former.