I like Alternate Universes in fanfic a lot, so I've collected recs for my favorites in this genre. I read gen, slash, and het in different fandoms, so you'll find all kinds of AUs recced here.
Within a fandom the recs are sorted by author, with new additions being marked. For TS the links are also sorted by the type of the AU (see sub-categories), but in the end I was too lazy to adopt that system for the other fandoms that have accumulated many entries. It is labelled whether something is gen, slash or het, but those are not separate sections. If you are interested in what I think works as AU and what doesn't, or what I count as AUs and what not, and a detailed explanation of what I see as sub-categories and why, you can read my thoughts on these subjects.
Some of my favorite AUs are WIPs, and some of them are probably likely to stay in that state, nevertheless I will also rec those. While I'm not particularly bothered by reading unfinished stuff, I know other people don't like doing that, so I'll indicate in the rec if it's still unfinished.
[Andromeda] [Avatar the Last Airbender] [Babylon 5] [Buffy/Angel] [DC Universe] [Due South] [Eagle of the Ninth updated ] [Farscape] [Harry Potter] [Highlander] [Lord of the Rings] [Merlin] [Multifandom] [Numb3rs] [Roswell] [Sanctuary] [The Sentinel] [Sherlock updated ] [Smallville] [Stargate: Atlantis updated ] [Star Trek: Reboot] [Star Trek: TOS] [Star Wars] [Supernatural] [White Collar] [The X-Files] [X-Men updated ]
Fighter, by PlaneJane. Slash, Marcus/Esca. (ca. 65,300 words)
This is for the movie I haven't watched, and it is a modern AU on top of it, so it read somewhat like original fic, but the whole setup worked well for my kinks: Namely, Marcus is an undercover police officer who infiltrates a slave-trafficking ring that organizes cage fights. He stops Esca from being killed in a fight and thus gains a slave.
Strangers, by cj_ludd18. Slash, Sherlock/John. (ca. 34,000 words)
Another robot AU, this one with robot!Watson. I wanted to punch Sherlock a lot for being a jerk in this, but that rather fits with his characterization, so it's not really a complaint.
Almost Human, by esteefee. Gen. (ca. 30,200 words)
This a robot!Sheppard AU, with a Rodney who doesn't trust the AIs. I was wary of the fic due to all the author warnings, because breaking of trust between my favorite characters (and mindcontrol not written as kink) risks running into my partner betrayal squick, but I like the cyborg/robot trope so I gave it a try and this worked well for me overall with the way it resolved things.
never too late to be who you might have been, by acetamide. Slash, Charles/Erik. (ca. 19,600 words)
This is a fix-it via time travel, i.e. Charles and Erik from shortly before Cuba are transported into the future to the time X2, see how things turn out between them and then do better.
your head caught in a waking dream, by addandsubstract. Slash, Charles/Erik. (ca. 23,100 words)
The scenario here is that Charles' parents had him committed to a mental hospital, which did not help much with his telepathy. Eventually Raven (whom he met like in canon) manages to break him out with Erik's help, and they hunt for Shaw.This is great h/c and I enjoyed how much damage was done to Charles and how he's slowly healing, while hunting for Shaw with Erik and Raven and killing people with his brain.
Extended Jam 'verse, by aesc. Slash, Charles/Erik. (ca. 27,000 words so far, the second story is still a WIP)
In this AU series mutants are publicly known, and thus in the late 1960s our characters find themselves in the middle of the mutant rights movement as part of the broader social movements, rather than in the middle of superhero/villain fights.
Peregrine, by Aeshna. Slash, Charles/Erik. (ca. 6,500 words)
This is wingfic, with a winged Erik. This has lovely detail, and I liked that Erik still has his regular powers too.
Try, Try Again by and_backagain. Slash, Charles/Erik. (ca. 5,680 words)
A Groundhog Day AU, in which Erik eventually manages to fix the outcome.
Remedial Dragon Training 030, by Anon. WIP
I don't know the How to Train Your Dragon movie with which this is a fusion, but Dragon!Erik is quite awesome.
Searchlight, by Anon. Slash, Charles/Erik. (ca. 2,100 words)
This was absolutely creepy and terrifying, yet awesome. It's an AU in which mutants are dehumanized and kept in research settings and the report-format of the story was ideally suited for this, and I liked the ambiguities that came with it, even though I normally dislike that in fic. Also check out the sequel Methods of Deduction by tawabids in the same thread, which is good as well.
Faults for Fixing, by beren. Slash, Charles/Erik. (ca. 25,500 words)
In this Charles makes contact with a mutant with precognition via Cerebro and sees the possible canon future, and prevents it from coming true.
The Shadow of the Moon Won't Do, by brilligspoons. Slash, Charles/Erik. (ca. 1,200 words)
This is a straightforward alternative to the beach scene, but a lovely example of this genre.
Hellfire AU, by Cesare and helens78. Slash, Charles/Erik. (ca. 54,700 words so far in three finished stories, but the series is still a WIP)
This is a modern day period dystopia in which mutants are enslaved, but Charles and his group are part of a mutant resistance.
Night Fishing at the Seine, by furius. Slash, Charles/Erik. WIP
Charles and Erik meet in Paris before the events of XMFC. I'm enjoying the atmosphere of this, and so far am intrigued by the plot.
Not Half As Blinding, by keire_ke. Slash, Charles/Erik. (ca. 29,500 words) In this AU Charles dies a comic book death from which he gets better eventually. But meanwhile Erik doesn't leave the others.
Big Fish Little Fish, by lilacsigil. Gen. (ca. 5,600 words)
In this AU Erik's comic-verse human daughter Anya is alive, and we see how events of the movie change (and what turns still out the same).
Puzzle Pieces, by lilacsigil. Gen. (ca. 15,000 words)
Here Darwin's death was of the comic book death variety, and Magneto & Co. realize that he can be put together again. Things go wrong and it's up to Mystique to organize a rescue, and to cooperate with Charles.
Three Kinds of Learning, by luchia. Slash, Charles/Erik. (ca. 16,500 words)
This is a nice mix of adventure with some humor. Erik tries to recruit Charles to his Brotherhood, after Raven introduced them, and then they are pulled into an adventure as Raven goes missing.
Skin Deep by manic_intent. Slash, Charles/Erik. (ca. 29,400 words)
A werewolf AU. It startled me a bit that Charles shifts into a female wolf despite being a male human, but it worked quite well, and I liked the worldbuilding.
Tessellation, by nekosmuse. Slash, Charles/Erik. (ca. 116,700 words)
In this AU both Erik and Charles are mutant rights activists. Erik is based in Genosha, and more militant than Charles, but he sort of has a crush on Charles whose writings inspired him. They meet at an event and things between them proceed from there, along with a good action-adventure plot.
No Yesterdays On the Road, by pocky_slash. Slash, Charles/Erik, Moira. (ca. 42,275 words)
This is a fix-it story in that its premise is that Erik stayed after Cuba to help build the school, but the bulk of the reconcilliation in the story is between Erik and Moira, who have to team up to find Charles after he suddenly vanishes.
MCIS: First Case, by Pookaseraph. Gen. (ca. 25,000 words)
This a modern AU, a fusion with NCIS I suppose, which I don't know, but I read it as just an government mutant agents AU. Erik is an agent, Moira his boss, and she partners Charles with him. The author says it's the first in a series that will be Charles/Erik, but this first is gen.
Taken By His Majesty, by Pookaseraph. Slash, Charles/Erik. (ca. 27,500 words)
Erik is a Roman legionnaire taken captive in Britain by the Celtic leader, Charles.
The Weight of Water, by pprfaith. Het and slash, Charles/Raven, Charles/Raven/Erik. (ca. 51,000 words)
This isn't too far from canon in the setup, except that Charles forms telepathic bonds, and the consequences of that are really well explored here, not just as romance ploy, but also the scary implications, both of Charles being powerful and subtle effects which accumulate and change all three of them.
Limited Release, rageprufrock. Slash, Charles/Erik, Hank/Alex. (ca. 58,000 words)
Another one I've recced before, but now it's finished finished and posted on the AO3, so it's worth pointing out again. It's a loose fusion with White Collar in which Erik is a mutant in the FBI and Alex is a mutant criminal, released to help him hunt for Shaw. It doesn't try to match up with the White Collar scenario completely, but has good worldbuilding and fun plot.
Imaginary Life Journey, by renata_kedavra. Gen, with implied Erik/Raven, Charles/Erik. (ca. 9,000 words)
Two scenarios in which Erik and Raven, and Erik and Charles respectively, try to recruit Kurt Wagner. This just has a lovely atmosphere (and the bits in French and German actually add to that and work), and is a good character study contrasting Kurt and Erik.
Mr. Xavier's Neighborhood, by SharpestScalpel. Slash, Charles/Erik. WIP
This is a series of snippets is adorable. Erik is raising Pietro and Wanda and has a crush on Mr. Xavier who hosts a mutant-tolerance children's show.
New Beautiful Things Come, by singlecrow. Slash, Charles/Erik. (ca. 17,600 words)
This is a modern AU with mutants being public in which Erik has a kosher bakery. It wasn't a setup I expected to get into, but the atmosphere and worldbuilding works, and it's a happy making story.
Brighter Path, by SisterMu. Slash and implied het, Charles/Erik, Erik/Raven. WIP
I had a bit of trouble getting into it, because the first chapter is a sex scene that didn't interest me much on its own merits. Though it made more sense to be there later on. In this AU Erik stays after Cuba, and they work out their ideological differences not through competing mutant teams but in strategy discussions while dealing with the practical concerns of the aftermath together, i.e. getting Charles care, dealing with the CIA and so on. I also enjoyed this take on Moira and the original character that appears.
Humane Society, by smilebackwards. Slash, Charles/Erik. (ca. 10,000 words)
A delightful kitten!AU, now finished and reposted from the kink meme. The author sums it up as "Basically, mutant supremacist Erik gets transfigured into a kitten, human Charles takes him in, and Erik really can't help falling in love." I couldn't describe it better.
Center of Balance, by soundslikej. Gen. (ca. 1,600 words)
This is a five things story with the theme "five mutants Charles Xavier never met at age 12, and one he did" and the snippets are a great mix from sweet to creepy.
Synthesis (Scenes from an AU), by starlady. Slash, Charles/Erik. (ca. 15,200 words)
The author claims this is not a fix-it for the ending, but it definitely is a reality where Charles and Erik are not on opposite sides in the future, and Erik stays rather than leaving, without any radical premise shifts (like the AUs below). So that counts as fixed in my book.
Show Me Your Teeth, by tawabids. Slash and het, Charles/Erik, Charles/Moira, Raven. (ca. 26,500 words)
Another werewolf AU. In this one Erik is a werewolf, Charles a werewolf hunter and they team up against Shaw. Also, don't miss the short epilogue that is in a different thread.
Possible Worlds, by trailingoff. Slash, Charles/Erik. (ca. 12,000 words)
This is a fix-it via a mutant-ex-machina do-over, or rather it takes even more than one try, and I like that they have to work to make things right.
Linger by waldorph. Slash, Charles/Erik. (ca. 29,700 words)
This is also a modern AU with mutants being public, in which Erik hears Charles in the apartment he rents, like a ghost haunting it. I liked the ensemble plot in this.
A Family Portrait In Progress, by Xris. Slash, Charles/Erik. (ca. 47,700 words)
This is not so much a direct fix-it as a later reconciliation, in which Charles ended up raising Lorna initially without knowing she's Erik's daughter. It's a series with two finished stories so far.
Dead Man's Paradise, by Yahtzee. Slash, Charles/Erik. (ca. 24,000 words)
The setup is inspired by some anime series I don't know. Basically mutants who are imprisoned are used in gladiator fights for entertainment purposes, and one of those places is run by Shaw. Erik ended up there because he killed a Nazi, Charles got himself imprisoned looking for Raven. I liked that it started rather dark, but then ended more hopeful. I also liked that the dehumanizing setup twists people (sort of a Stanford prison experiment) but that Charles showing solidarity changes things for the better, so it's not completely bleak for all the dystopia.
Enigma, by Yahtzee. Slash, Charles/Erik. (ca. 11,100 words)
Erik goes back in time, but the turning point here is not Cuba but he goes back to before his mother died, becomes a WWII mutant hero, "Enigma", and changes his life as well as history of human-mutant relations.
Undone, by Yahtzee. Slash, Charles/Erik. (ca. 6,600 words)
Another time travel scenario. Here Charles consciousness from post-X3 goes back to his younger self just after Shaw's attack on the CIA.