Andromeda

Not the Same, by Jane St Clair. (16 K)
A series of vignettes written for the Five Things That Aren't True challenge. Harper-centric.


Avatar the Last Airbender

Enslaved by sharkflip. Het, Katara/Zuko. WIP (ca. 104,500 words so far)
In this AU Zuko is captured by the Water Tribe and adapts. It's still a WIP and I'm enjoying the worldbuilding with the Water Tribe, though I'd really like to find out more about when and how the war went differently in the past on the larger scale. Still, it's very enjoyable.


Babylon 5

2284, by John Hightower. Het, John Sheridan/Delenn, David Sheridan/f. 2284, is finished in six parts, but the following arc in this AU, 2885, is still a WIP.
I admit that I have some problems with this series: the characterizations, especially that of Delenn, aren't quite as I see them, though they are a view of canon that I followed readily enough for the duration of the series and nowhere near the kind of bizarre pod-personalities one sometimes encounters in fanfic; in addition to that the romance parts of the story are OTT sometimes, with longish love declarations and internal insecurity monologues that border on the purple in places, and everybody has a tendency to burst into tears far too often. So why do I still recommend this? Because it has a compelling plot, which like canon incorporates romance but is really about how the personal choices influence the whole universe, because this AU is an alternative that I can see taking place in the B5 world (though I will admit that I haven't rewatched B5 in a while, so purists may have more objections), but mainly because it is written well enough that I rather stayed up through a night reading on than to put it down, despite all its problems.


Buffy/Angel

Season Noir, by Anna. Buffy/Spike, Anya/Xander, Willow/Tara. Individual episodes are finished, but the season is still a WIP. (ca. 321,100 words)
It's a fabulous virtual season eight, in a universe that according to the notes has branched off after the season six episode "Gone". The voices are spot on, the characterization fits and is consistent, there are demony plots and plans for world domination... It's one of those rare Buffy fanfics that really does the series justice, with all characters, with plots, with villains, and in places it just goes a little further, the way fanfiction can when television can't. I'm looking forward to the rest of the series (okay, I'm biting my nails and checking the page compulsively <g>).

Sidelines, Sidelines - The Other Half Lives, and Sidelines - House of Many Hearts, by Anna. Slash, Xander/Spike. (ca. 79,000 words)
It is an alternate version of season four, and many canon events are referenced (in slightly altered form) but not retold in detail, so it helps to remember those events to follow the story. I certainly noticed where I have gaps in my knowledge and reading it made me want to rewatch season four. Still I had no problems following the main story, which focuses on X/S, so you should read this even if your memory of season four isn't perfect. This bit from the author's notes sums up the premise quite well: "[...] I've always imagined that season four could be plausibly rewritten with Xander going through the Big Gay Change instead of Willow, with Spike replacing Anya as the demon of his affections. In some ways, a coming out drama makes more sense to me as an extrapolation of his previous characterization than it does for Willow's. [...] "

Wesley Rogue Demon, by Mad Poetess and James Walkswithwind. Slash, Wesley/Gunn. (ca. 26,250 words)
It's a season 2 AU and Wesley here isn't what he seems. I'm not sure the story would have worked as well for me if I didn't have a D/s kink (I'd like to think so, but as always with the own kinks it's hard to judge). It's not that there are kinky sex scenes, in fact there is no explicit sex at all, but Wesley's (AU) heritage that the others find out about comes with a lot of baggage, to put it mildly, and Wes has to confront and overcome that. (also on AO3, needs an account)

Phoenix Burning, by Yahtzee. Gen (with some Buffy/Angel).
Buffy is called back from the dead, but the world awaiting her has changed a lot. (also on AO3

As Time goes By, by Yahtzee. Het, Buffy/Angel, Angel/Cordelia, Wesley/Fred (all non-explicit).
A prophecy was fulfilled, the Venareth arrived, and with it the Powers brought the balance of good and evil, granted Angel his humanity and Cordelia visions without pain...so all is well? Not hardly, obviously in balance evil is much better off than it was before, and Wolfram & Hart stronger than ever. A really great future fic with an enthralling plot.


Due South

Pas de Deux, by Sihaya Black. Slash, Fraser/RayK. Het, Fraser/Victoria (off-screen). (276 K)
Ray Kowalski chose to become a dancer instead of a cop, and meets Fraser as a dance instructor. Fraser and Vecchio have (mostly) their usual biographies, and are still (work) partners when this story takes place. And the setup actually works. I could see this AU's RayK, and there are lots of vivid details, making his different life and past real to the reader. The story doesn't suffer from the "romance in a bubble" syndrome, either, even though it is from RayK's perspective, there is for example police stuff going on that impacts all of them. (Unfortunately I don't have a working link to this one any more.)

Sheepskin, by theleaveswant. Het, Diefenbaker/Francesca. (ca. 7,400 words)
This has a really cool premise, i.e. that Diefenbaker is a lycanthrope who is a human once a month, and a wolf the rest of the time.


Eagle of the Ninth

Dealing with the Consequences, by nemo_r. Slash, Marcus/Esca, Marcus/Esca/Seal Prince. (ca. 61,160 words)
In this AU Marcus and Esca don't kill the Seal Prince, but capture him.

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.


Farscape

No Dominion, by Maayan. Het, John/Aeryn, Stark/Zhaan. (480K)
This AU branches from canon after the episode SoD, they're trying to save Zhaan, but of course nothing is ever easy for Moya's crew.

Unrealized Peacekeeper, by OneEye. Het, John/Gilina, John/Aeryn. (over 178,000 words) WIP
This AU is inspired by the scene in the Farscape episode Unrealized Reality in which we glimpse the possibility of Crichton as a Peacekeeper captain. It's a very plausible background for how that could have come to pass through just a small change, i.e. what if the wormhole that brought him to the UTs deposited him about ten feet to the right of his original exit point. And this works actually without making Crichton not like himself in any way, nor does the story gloss over the Peacekeeper's ideology and actions we see in canon. Besides it is a great action-adventure that incorporates a lot of elements and events from the episodes.

UFO, by The Right Brain. WIP
The story takes place about a cycle after DWTB and explores an alternate scenario to season 4 and how John might get back to Earth. So far (it has 22 chapters at the moment) I quite like how the common Farscape (fanfic) topic of John getting home plays out in this version.


Highlander

Shades and Echoes, by auberus. Slash, Duncan/Methos. WIP
I liked the premise here that Duncan and Methos meet earlier in Methos' time in the Watchers. Not least because I like Methos & Watchers stories, and also there just aren't enough stories with Don Salzer still alive. Unfortunately this may have been abandoned because the last update was in 2009. OTOH the interval between chapter 11 and 12 was almost a year, and I've seen longer hiatuses before. Still, not the most likely candidate to be finished soon. ETA: It was updated in 2014 with chapters 13-19, so not abandoned after all. (also on AO3)

And Then Some, by Loch Ness. Slash and het, Duncan/Methos, Duncan/Amanda, Methos/OFC, Methos/OMC. (ca. 138,000 words)
In this AU Methos and Duncan have their first encounter during WWII.


Lord of the Rings

Back to the Beginning, by Adina. Slash, Legolas/Gimli. (48K)
Starting from a passage in the LOTR Appendix on dwarves and their belief that Durin was reborn several times, this AU explores what might be if Gimli was reincarnated too, and Legolas -- instead of sailing West -- decides to stay in Middle Earth to find each of Gimli's incarnations.

A Bit of Rope, by Aiwendiel. Gen. (ca. 387,000 words)
In this AU Gandalf doesn't fall in Moria, and this leads the Fellowship eventually down a darker part. This surprised me a bit at first from a divergence that seems is not something going worse, yet the events are plausible and gripping.

No Man's Child, by Anoriath. Het, Aragorn/OFC. (ca. 187,600 words)
The premise of the story is that a few years before the Ringwar in wake of suffering a serious injury Aragorn bows to pressure from the Dunedain to take a wife and produce an heir to secure Isildur's line, but it does not change that Aragorn loves Arwen. The story then mostly follows how the OFC dutifully reorganizes his household, and tries to manage politics and feudal obligations among the remnants of the Dunedain with a good amount of vivid detail, because besides wanting an heir, Aragorn asked her help keep his remaining people safe while Sauron's threat grows, yet he is mostly away doing the things he does in canon at this time, i.e. hunting for Gollum, which the reader knows, but the OFC doesn't in any detail. All of which is fairly bleak from a romance angle, but from a certain kind of loyalty and service kink perspective it is a delightful wallow, because the OFC acts the whole time in the service to her lord, and while companionship grows between them over time the status difference is never forgotten, and meanwhile Aragorn is seen to act in service to his people even against his own desires, because it is his duty to secure his family line. So that satisfies twice over. It is also great if you like stories of ordinary folk's everyday life against the backdrop of the build up to the Ringwar. (the link above needs an AO3 account, though it's also available unlocked on Stories of Arda)

Lie Down in the Darkness, Rise up from the Ash, by Dwimordene. (ca. 279,000 words)
The blurb describes this AU's premise as "without Gollum, how does the Quest turn out?", however the fellowship in this AU has worse luck than in the book in ways that are not easily connected to Gollum's early death. Which is explained as a result of a spreading dissonance in the Music of the Ainur from that death onward. It is not my favorite among Dwimordene's stories (but then for LOTR unlike for other fandoms, I'm not much in favor of AUs in general), but I enjoyed the story. Especially a bit further into the plot when more things are different, and there are less jumps, where those events remaining the same as in the original aren't retold in the AU. (The link above is the former HASA version, and now needs an AO3 account, though it's also available unlocked on ff.net, but missing an additional last chapter there)

Bond of Honor, by Meri. Slash, Éomer/Haldir. (ca. 25,500 words)
Considering that I have almost no interest in either Éomer nor Haldir I was a bit surprised that the story drew me in. But I do like the "accidental bond" trope, which these two have to cope with here as a side effect of a healing, especially when it comes with a culture clash as it does here.

Old Man Willow, by Nath. Gen. (ca. 1,200 words)
This is a short but creepy and surprisingly plausible scenario of what might have happened if Old Man Willow had been seduced by the One Ring and trapped the hobbits to get it. I really enjoyed the unusual perspective.

Webs, by Roz Kaveney. Gen. (ca. 680 words)
A dark AU, giving us a look inside Shelob's head, set in a universe where events turn out really well--for her. (also on AO3, needs an account there)

The Long Road Home, by Scribblesinink. Het, Boromir/OFC. (ca. 95,500 words)
This is one of the many Boromir-survives AUs, but a good one. I liked it as post Ringwar story dealing with the aftermath, and the original characters are engaging, but don't detract from the main interest in Boromir, Faramir and Aragorn.

King under the Mountain, by Zara Hemla. Gen. (ca. 2,860 words)
It's a dark and creepy AU set in a Middle Earth where events in The Hobbit turned out differently. It's quite short, and the backstory and its consequences for the current Middle Earth are more hinted at than fully explored, yet the set-up still comes across as eerily possible. BTW, I found this story thanks to the great Polyamorous Recommendations. (needs an AO3 account)


Merlin

The Peasant King, by a8c_sock. Slash and some het, Merlin/Arthur, Balinor/Hunith. (ca. 37,000 words)
This rec comes with the caveat that the story misses the final editing polish (I'm not assuming this merely because of the remaining typos, but because some beta notes in brackets are still in the posted version), so you need a certain level of tolerance for this. However the premise is quite cool in that Ygraine survives rather than Uther, and flees with her infant son to protect him from the ensuing chaos. Arthur grows up with Merlin and Will, and eventually he tries to win back his throne.

The Young Dragonlord, by Eldee. Gen, with some background Balinor/Hunith and Uther/Ygraine. (ca. 58,000 words)
In this AU Balinor stuck around to raise Merlin. I enjoyed both the background story and how this changed the present.

Loaded March, by Footloose. Slash, Merlin/Arthur. (ca. 490,420 words; the series is a WIP, the individual stories are complete)
This is a modern AU in which they are soldiers, but with magic still existing. I actually haven't gotten around to reading the last novel-length part, but I liked the worldbuilding and the action-adventure iirc overall.

Post hoc, ergo propter hoc ('After this, therefore because of this') , by hitome_bore. Slash, Merlin/Arthur. (ca. 95,000 words)
This mixes Merlin with The Sword in the Stone, that is Arthur finally finding out about Merlin's magic has gone horribly wrong, so Merlin decides to time travel and befriend a younger Arthur as his teacher. (an revised version is on AO3, but that is not finished yet.)

Arcane Asylum, by new_kate. Slash, Merlin/Arthur, Merlin/Edwin. (ca. 126,000 words)
I can only rarely get into Modern AUs in Merlin, but this one has great worldbuilding. It still has magic and prophecy and all the fun stuff, and both characters and certain plot elements form the series were transplanted well into the present day, without it seeming forced or too contrived.

Let Us Dare, by kianspo. Slash, Merlin/Arthur. (ca. 29,500 words)
In this AU Uther died instead of Ygraine when Arthur was born. I enjoyed how canon adventures where mixed into this different Camelot.

Leashed, by Riventhorn. Slash, Arthur/Merlin. (ca. 12,800 words)
The premise here is that Uther doesn't kill all sorcerers but enslaved some. Admittedly slavefic AU with mindcontrol elements is sort of like catnip as far as my kinks go, but this is not a kink wallow. (also on AO3)


Multifandom

Flowers in Your Hair (Four Characters Who were Never Hippies, and One Harsh Reality Check), by Kokiri. Gen. (ca. 2,600 words)
I don't know Legend of Zelda, but the HP, DC and Avatar parts were all great fun. Also worth looking at are the illustrations.


Numb3rs

Breaking the Code, by jlm110108. Gen. WIP (ca. 57,500 words)
This is still a WIP, but I'm really enjoying it so far, and it seems to get updated fairly regularly. I don't know the series it is a crossover with, Foyle's War, but I like the AU premise here that has Charlie as cryptographer during WWII and Don as American soldier.

Lucky by Leah Harper. Gen. (ca. 24,500 words)
In this AU Don and Charlie's estrangement lingers longer, and I enjoyed this angstier version of their relationship.

Sacrifices of the Keeper, by Pygmymuse. Gen. (ca. 28,340 words)
In this AU Don and Charlie's parents are killed in a car accident, when Charlie is still a teenager. (Unfortunately I don't have a working link to this one any more.)

The Fugitive, by Zubeneschamali. Gen, Don Eppes. (ca. 144,900 words)
This AU is based on the Fugitive plot. Don has been framed, and was convicted for a murder he didn't commit, and is now on the run to prove his innocence.


Roswell

Persephone's Footfalls, by Elizabeth. Het, Michael/Maria.
The aliens landed openly in Roswell in 1947, there has been an war and the aliens won...but did they really? Inspired by the Persephone myth, but it's a genuine sf story.


Sanctuary

The Road Not Taken, by Penknife. Het and slash, James/John/Helen, Helen/Nikola. (ca. 4,000 words)
This has the cool premise that the energy creature possession goes differently, and John Druitt doesn't become Jack the Ripper. (needs an AO3 account)


Sherlock

The Republic of Heaven, by blind_author. Slash, Sherlock/John. WIP
This is meshes His Dark Materials with Sherlock, and incorporates a bit more of the HDM worldbuilding than just dæmons. (also on AO3

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.

Gone Is My Past, by cyerus. Gen, John Watson, Mycroft Holmes, Sherlock Holmes. (ca. 8,000 words)
In this story John used to be a bomb detection dog who was turned into a human. I was recced this when I asked on kink-finders for stories featuring forced human-animal-hybridisation, and though this is rather the reverse, it pushed the the same kink of non-consensual body modification angst and h/c for me. And of course dog!John pushes certain D/s buttons too. (also on AO3)

Asterioidea and Highly Intelligent, Observant, and Destructive When Bored, by etothepii. Gen, Sherlock and Mycroft, and Slash, Sherlock/Watson. (ca. 1,850 and 5,000 words)
This is a His Dark Materials fusion with a great twist. (also on AO3)

Show Me How to Stop Running, by etothepii. Slash, Sherlock/John. (ca. 12,400 words)
As anyone following my recs knows, I love werewolf AUs. John gets bitten by a werewolf in Afghanistan and comes back to London where he meets werewolf!Sherlock. (also on AO3)

You Call Me Like the Moon, by etothepii. Gen, John Watson, Sherlock Holmes. (ca. 3,000 words)
Another werewolf!John AU by the same author as the one above but a different scenario, in that John was a werewolf before Afghanistan and Sherlock isn't, and worldbuilding for the lycanthropy is different too. (also on AO3)


Star Wars

Silent Faction, by analise and Kirby Crow. Slash, Qui-Gon/Obi-Wan, also Obi-Wan/f.
The authors warn that this one has a real plot, though I see this more as a strength... It is a couple of years after TPM, Obi-Wan and Qui-Gon are both alive, but estranged. This story paints a vivid picture of an alien society on the mining moon of Ramos V, and it is one of the rare stories, where they really get to be Jedi, complete with alien societies, diplomacy, conflict and the Force.

Five Things That Never Happened to Luke Skywalker, by Corana. Gen and het, Luke/Mara. (ca. 6,800 words)
A look at five other possible lives Luke Skywalker could have had, and all are plausible.

Exiles Universe, by DBKate and Kass. Slash, Qui-Gon/Obi-Wan.
It's post-TPM, Qui-Gon is alive, he and Obi-Wan are in exile on Tatooine, because the Jedi order still crumbled, and Anakin still turned to the Dark Side. Tatooine comes alive in those stories, which capture the harshness of both the planet and Palpatine's Empire.

In the Moment, by dee. Gen. Obi-Wan, Qui-Gon. (ca. 2,600 words)
In this AU Qui-Gon survives, but the focus isn't on what will happen after, but on what could have led to his survival. (also on AO3)

Some Things Are Certain, by dee. Slash, Anakin/Obi-Wan. (ca. 7,300 words)
Qui-Gon and Obi-Wan didn't meet and free Anakin during TPM, and he remained a slave and never left Tatooine. Years later Obi-Wan's ship breaks down on Tatooine. (also on AO3)

Elements Series (Water, Earth, Air, and Fire), by Lilith Sedai. Slash, Qui-Gon/Obi-Wan.
Qui-Gon did not take Obi-Wan as his padawan on Bandomeer, instead he became Yoda's apprentice. It has a touch of yenta!Yoda, IIRC, but I liked this series a lot.

Redemption, by Marnie. Gen, Obi-Wan, Anakin, Qui-Gon, Dooku. (ca. 21,600 words)
It's a time-travel story, that explores what if the Jedi Council had found a way to send Obi-Wan and Anakin back in time to assassinate Dooku, because they thought that was the only way to prevent greater bloodshed. But it is before his fall to the Dark Side, back when Qui-Gon was still his apprentice, and he obviously doesn't approve of a solution like that. I was a bit dubious about the set-up at first, but I liked how the characters struggled with difficult choices, looked for alternatives, and the changes are quite believable. (also on AO3)

The Path Not Walked, by Nati_A. Gen, Obi-Wan, Qui-Gon, Anakin. (ca. 62K) WIP (and quite likely to remain unfinished seeing how it hasn't been updated since 1999 or so...)
This is a retelling of TPM, but in a universe where Obi-Wan wasn't taken as an apprentice by Qui-Gon and now works in the AgriCorp, helping Naboo as an expert. I found this take on the scenario interesting because Obi-Wan is successful in the AgriCorp, rose through its ranks and while he regrets not becoming a Jedi he isn't deeply unhappy with his task as an agricultural expert either. It's a bit exposition heavy in some section, when the characters reflect the past, but I didn't mind that much, because the AU was interesting, though I sometimes wished the author had found a way to show the past rather than have the characters think about it.

Meet another, by torch. Slash, Qui-Gon/Obi-Wan. (ca. 66,500 words)
Another one where Obi-Wan did not become Qui-Gon's apprentice, but in this one Qui-Gon ended up in the hands of Jabba the Hutt, where Obi-Wan finds him on a mission to Tatooine.


Suits

The New Deal, by Closer. Gen. (ca. 33,500 words)
In this AU Harvey and Mike meet earlier than in canon. Harvey is still a student and Mike a teenage runaway.


White Collar

Always Starts the Same, with a Boy and a Girl, by lightgetsin. Slash and het, Neal/Peter/Elizabeth. (ca. 21,500 words)
In this AU Elizabeth met Neal first rather than Peter, and things turn out differently for them. This quite charming and had a nice symmetry to canon without being too contrived.


The X-Files

The Magician, by Jennifer Lyon and Suzanne Bickerstaffe. Het, Mulder/Scully.
When this was recced to me I was sure I'd hate it: It is a Fantasy AU, it is MSR (when my X-Files preferences are normally NoRomo), it lands Mulder and Scully (in a rather deus-ex-machina way) in a land where magic works and a number of other things are very strange. I know, I know, it sounds rather awful, but the authors make it work, because Mulder and Scully are as bewildered as the reader, it is interesting and sometimes funny to see how they deal with it. I actually enjoyed the first book most, and lost a bit of interest after that. The author' site unfortunately vanished but The Magician I (and the following books) are still at The Annex: X-Files Novel Archive in a PG-13 and a NC-17 version.