The Aquarians (ca. 2,000 words) and its sequel Electric Kool-Aid, Add Fresh Paint (ca. 1,500 words), by Aesc. Slash, Rodney McKay/John Sheppard.
A hilarious story in which Rodney and John meet at Woodstock.
Faith Healing, by Aesc. Slash, Rodney McKay/John Sheppard. (ca. 11,300 words)
This AU has a really cool premise. John isn't in the military anymore, but has come across an ancient healing device. Rodney and Lorne track down rogue Ancient tech for the SGC.
I, Rodney, by Alex51324. Gen. (ca. 42,100 words)
A robot AU with Rodney as a robot. I especially liked that Rodney's "childhood" was not actually over the top tragic as far as fictional childhoods go (especially for AIs), despite his estrangement from his father/creator and family, and also that in retrospect his grown up perspective eventually evolves from the angry teenage AI.
Cycle and Circuit, by Alloy. Slash, Rodney McKay/John Sheppard. (ca. 8,500 words)
It's rare for me to read crossovers or fusions without knowing both sources, but this fusion putting John and Rodney into the universe of Avatar: The Last Airbender, pulled me in quickly and made the Avatar universe become alive and seem very vivid and fascinating even though I've never watched Avatar: The Last Airbender. I really liked the atmosphere, and the descriptions, and how John and Rodney were fit into this fantasy universe and its mythology.
Gypsies, Tramps, and Thieves, by Auburn. Gen plot with mixed slash and het elements, John Sheppard, Rodney McKay, Vala, Daniel Jackson, Janet Fraiser, others. (ca. 180,000 words)
This is simply an awesome space pirates epic mixing both SGA and SG-1 characters, and what's even better is that it reveals us their backstory so that it makes sense that the familiar characters end up this way. It has a great action-adventure plot and I loved the whole atmosphere.
Three Fates, by Auburn and Eretria. Slash and het, Rodney McKay/John Sheppard, Rodney McKay/Sheppard/Atlantis, Rodney McKay/Elizabeth Weir/Sheppard, John Sheppard/Atlantis. (ca. 161,700 words)
I adore stories with a sentient Atlantis in general, but this novel is truly extraordinary. In this AU the events surrounding the Ancient superweapon during Trinity unfold in a worst case scenario, and they tear a hole in the fabric of the universe, instead of "just" destroying a solar system. While their own timeline ends John, Rodney and Elizabeth are thrown into the past, and try to change the future while dealing with their guilt and isolation. This novel has a great plot and characterization, and is a fascinating take on Atlantis and the Ancients. (also on AO3)
Wrapped in a Red Ribbon, by Auburn. Slash, Rodney McKay/John Sheppard. (ca. 23,000 words)
This is a fun and action-packed non-stargate AU with John as a cop and Rodney as a forensic scientist who end up going undercover as a gay couple. The story skillfully weaves in a lot of characters from both SGA and SG-1 into its mystery plot, and though I didn't much like the way Ford turned out here, it worked for story. It's a great mix of humor and darker elements, and that the story fed my slave!John-kink certainly didn't hurt either. (also on AO3)
Promises of Return (ca. 3,155 words), Reflections on Return (ca. 3,500 words) and This Mortal Coil (ca. 6,630 words), by Azure_Horizon. Het, John Sheppard/Teyla Emmagan.
In this series Teyla didn't join the expedition, but stayed with the Athosians, and just has intermittent contact with John though they are allies. It's a bit bleak, but I enjoyed the John/Teyla relationship here.
All You Can Be, by beingothrwrldly. Slash, John Sheppard/Rodney McKay. (ca. 4,350 words)
Rodney is a music teacher, John was a pilot and gets recalled for war.
Honor and Country, by Bluflamingo. Slash, John Sheppard/Rodney McKay. (ca. 25,000 words)
This is a fusion with a series called E-Ring, which I have never seen. Basically it is a non-Stargate earthside AU, in which the SGA and SG-1 characters are military intelligence operatives. Rodney is in the CIA, John in the Army, and there is a tense conspiracy plot involving Kolya.
The Year That Was, by Bluflamingo. Slash, Cam Mitchell/John Sheppard. (ca. 11,390 words)
Cam hooks up with Sheppard in the alternate reality of the SG movie Continuum.
Wild Nest, No Prison (ca. 2,000 words), Sharp and Sided Hail (ca. 2,375 words), and I Am Not the Thing I Was (ca.2,500 words), by Brat Farrar. Gen, John Sheppard. The individual stories are finished, but the universe (with some more bits and fragments listed here in the "As Kingfishers Catch Fire" series) is still a WIP.
These are set in version of the SGA universe where magic works and is as commonplace as science, and I really enjoy how parts of the larger mythology shine through, but then I adore world-building.
The Convenient Husband (part 1) and part 2, by Brighid. Slash, John Sheppard/Rodney McKay. (ca. 12,400 words)
It's another response to the Harlequin challenge. John has to marry to inherit his share of his family's aerospace company, and his childhood friend Rodney seems the most convenient choice.
Here In This Lonely Place, by Brighid. Slash, Rodney McKay/John Sheppard. (ca. 4,500 words)
A fascinating and creepy dystopia, with interesting plot twists involving both the Wraith and the Asurans as well as the Ori. (also on AO3)
The New Mutants, by Brighid. Gen (so far), Rodney McKay, John Sheppard, Elizabeth Weir, Daniel Jackson, Jack O'Neill. WIP
It's a fusion with the X-Men. The government experiments on humans with the ATA gene and they develop superpowers. SG-1 and SGA characters run a kind of resistance that rescues people. It's not that far along yet, but the worldbuilding has me hooked already. (Sadly, I don't have a working link to the story anymore.)
A Hundred Happy Things, by busaikko. Rodney McKay/John Sheppard. (ca. 30,000 words)
Non-Stargate AUs always have a harder time to get me interested, because I like the action and SF elements, but this sucked me in completely even though it is a domestic AU, and a kidfic too. It's an earthside romance between Sheppard and McKay, who takes care of Madison (his career having been somewhat tanked thanks to a sexual harassment lawsuit), while Jeannie is pursuing her own career. The characters were all very human and real (including Madison who was smart but not annoyingly precocious).
Animal Husbandry, by Casspeach. Slash, John Sheppard/Rodney McKay. (27,438 words)
This was written for the Harlequin challenge. Rodney is a vet and John a rodeo cowboy, which sounds weird, and yet it works. (needs an AO3 account to read)
A Farm in Iowa and its sequels And Then There Was Finn and These Men Who Have Flown, by Cate. Slash, John Sheppard/Rodney McKay. (ca. 12,000, 8,000 and 18,000 words)
The idea to have John leave the military after some time in Antarctica, but before meeting O'Neill, just to move to a farm in Iowa he inherited from his grandfather may seem a bit odd, but in this case it really works. Since it's a slash story Rodney's car breaks down near John's farm, and a friendship starts to develop. This story is a delightful slowly building romance, fun to read, and has a great atmosphere with lots of vivid little details. (The whole 'verse is also on AO3.)
A new history of Captain John Sheppard, by Cate. Slash, John Sheppard/Rodney McKay. (ca. 16,440 words) This is a fusion with Temeraire, and just all around awesome. It's set in 1811 and Sheppard has been exiled to the new world breeding grounds where he found his dragon. (also on AO3)
None Can Quite Extinguish, by Cate. Slash, John Sheppard/Rodney McKay. (ca. 45,300 words)
This is a look at how things might have gone if there had been more survivors of Sateda, who then stayed on the planet. It has great world-building, and the internal politics of Sateda and the Genii in this story are interesting. (also on AO3)
The Difference Engine, by Copperbadge. Slash, Rodney McKay/John Sheppard. (ca. 22,000 words)
This AU was creepy, yet also funny. The premise was that John dies in Afghanistan and gets resurrected as robot via experimental SGC tech. And okay, I totally have a soft spot for "Sheppard as a robot" stories (though not because I think Sheppard was somehow emotionally stunted, but because robots are awesome), but this was just a quick and fun read.
Come Back Later, by Cottontail. Slash, John Sheppard/Rodney McKay. (ca. 8,800 words)
It's an alternative ending for Tao of Rodney.
Everything But Love, by Cottontail. Slash, John Sheppard/Rodney McKay. (ca. 24,200 words)
This story adapts the plot of the movie The Lake House. I have never seen that, but the crux of it is that John and Rodney get each others' mail, but are living two years apart. The time travel paradoxes in this one made my head hurt a bit, but then the time travel here is more a vehicle for their romance than the point of the story, and the romance was a lot of fun to read. (Sadly, I don't have a working link to the story anymore.)
we don't need roads, by Crimsonclad. Slash, John Sheppard/Rodney McKay. (ca. 1,750 words)
It's a short story that fuses SGA with Back to the Future in a surprising way that I don't want to spoil for you, however it gives Back to the Future a more sinister twist. (also on AO3)
Jungle Fever, by cupidsbow. Slash, Rodney McKay/John Sheppard, Cameron Mitchell. (ca. 8,900 words)
The story is based on a Harlequin romance prompt, and is an entertaining adventure story. I would have loved to find out more of the background and how exactly this universe differs from the canon SG-1. Apparently he SGC is fighting the Goa'uld on earth since Rodney has been kidnapped by some Goa'uld's servants and is then rescued by John Sheppard, and their jungle adventures and encounters with hidden Ancient tech proceeds from there. (also on AO3)
Mnemonic, or Four Ways John Sheppard Didn't Lose His Mind, by cupidsbow. Slash, Rodney McKay/John Sheppard. (ca. 3,650 words)
It's four brief AUs all with cool worldbuilding, and all dealing with a different kind of amnesia or altered mind. (also on AO3)
Absolute Corruption, by Cypher (seikaitsukimizu). Slash, Rodney McKay/John Sheppard, Daniel Jackson, Jack O'Neill, Lorne. (ca. 19,200 words)
It's an AU for the SG-1 episode Absolute Power. Daniel managed to keep control of earth, and Rodney works for him, while secretly trying to sabotage. Then Daniel gives him the captured resistance soldier John Sheppard as a "pet". I really enjoyed the plot twists in this stories, the uncertainty about who is on whose side. (also on AO3)
Expeditionary Conditions, by Domenika Marzione. Gen. WIP
It's a great look a how things might have turned out, had Sumner survived. This universe as a whole is a series/WIP but the parts stand well on their own.
East of The Sun, West of The Moon, by Dossier. Gen, John Sheppard, ensemble (there are some het relationships though they aren't the focus). (ca. 150,000 words)
This is simply an awesome SGA novel. The premise is that they don't quite have as much luck in the episode The Intruder, and the Daedalus is shipwrecked on a planet. It is John-centric in its POV, though it is very much an ensemble story, and the worldbuilding is fantastic. The alien culture is interesting and complex, the original characters are real people without taking away too much attention from our heroes, and it features Pegasus galaxy history and Ancient tech as background to the plot of the stranded Daedalus too. (also on AO3)
Nil Nisi Bonum, by Dossier. Gen, John Sheppard, Teyla Emmagan. (ca. 27,600 words)
It's a fusion with Lawrence of Arabia. It still takes place on Atlantis and in the Pegasus Galaxy, but events unfold a little differently for the expedition, for example Sumner doesn't die, so Sheppard remains largely outside the Atlantis military and goes partially native among the Athosians, thus making the plot about waging war against the Wraith resemble the movie. I'm not sure how close it is to the movie in terms of plot, because it's been ages sine I last saw Lawrence of Arabia, but the story works very well as an SGA AU that stands on its own. (also on AO3)
Calling Down the Lightning by Dreamwaffles. Slash, John Sheppard/Rodney McKay. (ca. 55,500 words)
In this AU magic is real, however because of its huge destructive potential people capable of doing magic get preemptively executed on Earth, so magic users try to hide their abilities, usually not with much luck as it manifests first for emotionally volatile teenagers. I enjoyed the premise and world quite a lot here.
Born in the Barrens, by Eildon Rhymer. Gen. (ca. 60,000 words)
It's no secret that I have a slavefic kink and a soft spot for amnesia fic, and here both go together like chocolate and hazelnuts. Still, I think even readers not sharing these kinks will enjoy this story for its good mix of angst, h/c, world-building, adventure and later on team interaction. (also on AO3)
Where the White Lilies Grow, by Eildon Rhymer. Gen. (ca. 44,400 words)
In this AU two alternate realities collide via a Stargate malfunction: a Rodney from an Atlantis that has been cut off from Earth without a Sheppard joining the expedition gets stranded (unfortunately with Wraith too) on an post-apocalyptic version Earth, where he runs into that reality's John Sheppard. (also on AO3)
The Roads Never Lead Where They're Supposed to Go, by eleveninches. Slash and het, John Sheppard/Rodney McKay, Radek Zelenka/Elizabeth Weir. (ca. 140K)
It took me a bit to get into this story's mix of pure wackiness and more conventional action-adventure, but once I did, it was a lot of fun. John is a botanist and Rodney is not head of the science team, Zelenka is, Carson has mental problems, and their hijinks are hilarious. (also on AO3)
Atlantis Wasn't Built in a Day, by eleveninches. Slash, John Sheppard/Rodney McKay. (ca. 3,600 words)
What if they hadn't found a way to save Atlantis from the hurricane during The Storm? This scenario could have been played very angsty, but this story goes for a more lighthearted look at the expedition having to cope with wilderness survival.
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.
Dead Like Them, by forcryinoutloud and Layton Colt. Slash, John Sheppard/Rodney McKay. (ca. 41,500 words so far) WIP
It's a fusion with the series Dead Like Me. John, Rodney, Ronon, Jack and Daniel are grim reapers. (also on AO3, needs account)
At The Hour When We Are Trembling, by Frostfire. Slash, John Sheppard/Daniel Jackson. (ca. 36,000 words)
In this post-apocalyptic AU the Wraith make it to Earth, and John and Daniel lead a resistance cell. It's very griping, I couldn't put the story down once I started. (also on the Ebook Library)
Separation Anxiety, by fydyan. Gen, John Sheppard. (ca. 1,000 words)
This short vignette explores why John might have decided not to join the expedition.
Carousel, by Gaia. Slash, Rodney McKay/John Sheppard. (ca. 13,000 words)
I'm a sucker for timetravel as well as stories dealing with ascension and this one has both. It's an AU version of the events from the Siege.
Curiouser and Curiouser, by Gaia. Gen. (ca. 4,300 words)
I wished this AU had been longer to really explore this world, but even as a short story the premise is great. In a reversal of the show's setup the Pegasus galaxy sends an interplanetary expedition led by Teyla Emmagan to search for the lost world of Earth, where the Ancestors are said to have gone, only to find Earth overrun by the Ori. The expedition, with Genii and Satedan forces find remnants of the SGC and set out to help their resistance against the Ori. I would have liked getting an epic chronicling their adventures, and seeing the conflict of the Pegasus expedition's goal to find weapons against the Wraith and Asurans, with the Milky Way priority of fighting the Ori, but this time with the Pegasus cultures at an advantage, and this story is too short to mor than tease with that, but very intriguing with its shift nevertheless.
The Wrong Side of the Tracks, by Gaia. Slash, Rodney McKay/John Sheppard. (ca. 15,200 words)
This story adapts the Disney movie plot "Lady and the Tramp" into a post-apocalyptic SGA futurefic, and I really don't want to spoil the fabulous twists and character mappings that make the two fit together. It shouldn't work so well, but surprisingly it does.
Not in the Stars, by greenconverses. Gen, John Sheppard, Teyla Emmagan. (ca. 3,900 words)
In this AU John is an Athosian and Teyla earth military. The story is mostly set pre-series, explores both their lives, and then ends with their first meeting.
See No Evil, by Greyias. Gen. (89,048 words)
In this AU events in the past happened differently so that there is no SGC (finding out what exactly changed is part of why the story is fun). John and Rodney meet while working for the same company, John as a testpilot and Rodney as a scientist. The plot here is fast paced and had me completely hooked.
Before & After, by helena_eternal. Slash, John Sheppard/Rodney McKay, Radek Zelenka. (ca. 3,610 words)
It's a Conversion AU told from Radek's POV in which John's change didn't reverse fully.
Love Is a Long Long Road, by Hily and Telesilla. Slash, John Sheppard/Rodney McKay. (ca. 40,000 words)
If you like romance mixed with kink this AU is right for you. John and Rodney meet in college, get together and start a D/s relationship (with John as submissive). There are even two endings to choose from, one more fluffy, the other more angsty. (also in AO3)
A Year in the Life, by ignipes. Slash, Rodney McKay/John Sheppard. (ca. 3,300 words)
It's an SGA AU set in the Supernatural universe. John and Rodney are hunters, and we gradually find out their backstories and how their lives turned out differently than in SGA.
Until Love Can Find Me, by Isagel. Slash, John Sheppard/Rodney McKay. (ca. 10,900 words)
This is another one in the growing genre of Vegas-verse AUs. I really liked this take on Vegas!John, and found it an interesting variant of possible futures there, because John survives but actually doesn't get recruited by the SGC.
Push and its sequel Pull, by Jane Elliot. Slash Rodney McKay/John Sheppard. (ca. 39,000 words and 27,000 words)
It's somewhat like a Harlequin romance story. Rodney, who works at the SGC, has an accident with Sheppard, who lives on the streets as result from his severe PTSD and dishonorable discharge, which circumstances are slowly revealed through the story. Then friendship and romance follow with a fair but not overwhelming amount of angst. (Sadly, I don't have a working link to the story anymore, though currently you can still find it cached on diigo here.)
Unconventional Beauty, by Jane Elliot. Slash, Rodney McKay/John Sheppard, Radek Zelenka/Jeannie McKay and Ronon Dex/Teyla Emmagan in the background. (ca. 30,400 words)
The story is a kind of The Beauty and the Beast remix with Stargate Atlantis elements. What I really liked was that it didn't just take the characters into the fairy tale but also kept the sf elements like the Ancients and the Wraith. (also on AO3)
Biggest Ever Sky, by jchalo and lilysaid. Slash and het, John Sheppard/Rodney McKay, Carson Beckett/Ronon Dex, Teyla Emmagan/Sora, and Teyla Emmagan/Aiden Ford. (ca. 11,000 words)
This is a great circus AU. The way it transfers the characters into a circus universe really works, but what I liked best was how the atmosphere of the story somehow captured the essence of circus, that is dreamlike and fantastical moments emerge out of an almost gritty down to earth reality and both seamlessly mix.
Strangers When We Meet , by Jendavis. Slash, John Sheppard/Ronon Dex. (ca. 14,000 words)
In this AU the expedition encounters a Sateda that didn't fall. I really like how the society was developed here, and seeing different aspects of Ronon. (also on AO3)
Crimes Against Humanity, by Jenn. Slash and het, mainly John Sheppard/Rodney McKay, also Laura Cadman/Carson Beckett, Teyla Emmagan/Elizabeth Weir. WIP
The characters here are quite different from their canon counterparts, because they are more or less ruthless supervillains, and Atlantis is used as a prison camp that is said to be inescapable. That is of course before they take over. However it is definitely fun to root for the evil twin versions of the team. (also on AO3)
Strangerverse, by Jenn. Slash, John Sheppard/Rodney McKay. The individual stories are finished, but the universe is still a WIP.
It's a quantum mirror story in which a Rodney from an alternate reality ends up in the canon universe, albeit at a point in the future after canon!Rodney has died. It is really interesting to see the familiar universe through the eyes of the other Rodney, and to slowly piece together all the ways how that universe, in which John was a mathematician and working as a scientist for the SGC, is different from the familiar one. (also on AO3)
The Best Things in Life Are Free, by Kajikia. Slash and het, John Sheppard/Rodney McKay/Ronon Dex/Teyla Emmagan. (ca. 3,800 words)
John and his team are con artists and have a run-in with his ex-wife, who works for the government. (also on AO3)
A Narrow Bridge, by Kass. Slash, John Sheppard/Rodney McKay. (ca. 18,430 words)
I thought this was one of the more unusual SGA AU scenarios I've encountered, and only in part because it's a non-stargate AU that put them in a yeshiva instead, which is quite a step from SF soldier hero with geek sidekick, but even more because it's unusual that in an AU John and Rodney do more or less both the same thing, rather than meeting by chance. Still I enjoyed the AU, and I liked the glimpses we got of their backstories (I'd totally read a prequel to this giving me more of this John's history).
Si Muovo by Kass and Sihaya Black. Slash, John Sheppard/Rodney McKay, John Sheppard/OMC. (ca. 39,400 words)
This has been widely recced already, so if you're inclined to give a somewhat unusual premise -- Rodney is a Jesuit priest and John a bush pilot, and they meet in Alaska -- a try at all you probably have already read this. Anyway it really pulled off a genuinely religious Rodney well, has an engaging plot (if slightly contrived, but it is Stargate after all) and a nice mix of angst, romance and quirky background atmosphere. (also on AO3)
Cage for Gods, by Kat Reitz and Perryvic. Slash, John Sheppard/Rodney McKay, Carson Beckett/Rodney McKay. (ca. 63,950 words)
In this AU Rodney has ascended in Tao of Rodney. I liked the story for its interesting view of the Ancients and ascension.
Splinters and Stones, by Kat Reitz and Perryvic. Slash, John Sheppard/Rodney McKay/Carson Beckett, Rodney McKay/Other, John Sheppard/Other. (ca. 100,800 words)
For the purposes of full disclosure, a big part of why I enjoyed this so much is that I have a slavefic and non-con kink, which is also why I liked the CSI story set in this universe by the same authors, which however was more focused on the kink aspects than this one. One of the main points of difference in this AU is that it has some kind of feudalistic structure with an imperial government and feudal houses, and people can be subject to certain kinds of slavery that works like debt bondage or indentured servitude. Anyway, even if you aren't into slavefic in particular, the world-building is very cool, and there is lots of plot and plenty h/c. (also on AO3)
The Blade and its sequel Aegis, by Kellifer_fic. Slash, John Sheppard/Rodney McKay.
John as a kind of bodyguard slave in a fictional feudal society really works for my kinks, but I'd like to think that this one creates a vivid world and is written well enough to be enjoyable even if it doesn't fit your kinks.
To My Destiny, by Kodiak Bear. Gen. (ca. 8,800 words)
In this AU Janus convinced the Ancients to allow the use of his time travelling technology and they took Atlantis into the future, to present day Earth, when they continue the fight. It's an interesting premise and the Ancients here are just the right mix of ruthless and creepy but not actually bad guys.
No Matter Where you Go, There you Are, by Kriadydragon. Gen, team. (ca. 6,600 words)
This is an apocafic with Goa'uld in the Pegasus galaxy and John arriving there by a different route than in canon. I found the worldbuilding premise really intriguing and would love to see a longer exploration, rather than just the initial meeting of John and the others, but I still enjoyed this.
A Wing and a Prayer, by Kriadydragon. Gen. (ca. 97,150 words)
An AU with dragon companions, how could I not like that? Okay, I guess some may argue dragons are overdone, but I like them still. Besides, this is a really solid action adventure, so you might want to give it a try, even if the dragons don't sell it to you.
Imago: The Tao of John, by Kristen999. Gen. (49,759 words)
John gets caught in the ascension machine in Rodney's place, and this version was fun to read and I liked how the superpowers were handled. (also on Wraithbait)
Choice of Duty, by Kyrdwyn. Gen, John Sheppard, Radek Zelenka. (ca. 4,680 words)
The premise here is that John is ex-military, and didn't join the Atlantis mission as military, but as a scientist. After Sumner's death, which happens later here than in canon, he's drafted back into active duty by Elizabeth. I'm not sure I see Elizabeth quite this way, but the interaction between John and Radek made this a nice read.
Circle of the Sun, by LadyAmarra. Slash and het, Rodney McKay/John Sheppard, John Sheppard/OFC. (ca. 42,300 words)
John ascends because of the Ancient machine in Tao of Rodney. The people with whom he ends up with when he eventually descends have been given an interesting background, and it was quite chilling to see John's loyalty brought to its final consequences here though I don't want to spoil the plot twists by being more specific. (also on AO3)
The Road To Nevada, by lamardeuse. Slash, John Sheppard/Rodney McKay. (ca. 38,000 words)
It's a WWII-era AU. John was pilot in WWI, and applies to work as a test pilot for Rodney, who's developing planes. However soon everything gets more complicated as they fleeing from Nazi spies who want Rodney's knowledge of the secret Stargate program. Their cross-country road trip makes for a great and sometimes funny adventure-story, and I enjoyed how the other SG characters were cast.
Dearest, by Lavvyan. Slash, John Sheppard/Rodney McKay. (ca. 4,200 words)
The people with the ATA gene are regarded as pets in this AU, though then it turned somewhat atypical for slave/mindcontrol fic (and has a sad ending), but it still worked for my kinks. (also on AO3)
Stargazing, by Lavvyan. Slash, John Sheppard/Rodney McKay. (ca. 4,200 words) In this story earth fought a war against aliens, and to win it modified its soldiers, which is the AU background for bug!John here (a trope which I love), and also used androids, so we get an android!Rodney. This story is set post-war, and they meet each other after their decommissioning while they cope with a society that is less than welcoming. I really liked the world-building here, even though we only get glimpses of the universe. (also on AO3)
Theory of Evolution, by Lavvyan. Slash, John Sheppard/Rodney McKay. (ca. 42,000 words)
It's another Conversion AU in which John's transformation isn't fully reversed. This one is long and has a nice amount of angst. Also, I just have a soft spot for Bug!John in general. (also on the Ebook Library)
Gods That Slumber (ca. 2,700 words) and its sequel Engineering the Fall (ca. 4,300 words), by Layton Colt. Slash, Rodney McKay/John Sheppard.
Another variant of the "John-as-descended-Ancient" premise.
Male Enhancement (The Soul and the Company Store Remix), by Leah. Slash, John Sheppard/Rodney McKay, Carson Beckett, Radek Zelenka. (ca. 46,500 words)
I've already recced this right after it was posted because I couldn't contain my squee long enough to wait for my next regular AU recs update, but if you haven't read it already you definitely should, because it is an awesome story with John as an AI, that is heart-breaking at times, but also funny in places, and just great reading all around. Don't miss the gen prequel/companion story Muscle and Blood and Skin and Bones, also by Leah, featuring Evan Lorne, John Sheppard, Cameron Mitchell, Radek Zelenka, and Bill Lee (ca. 18,100 words), or the sequels Another Day Older (slash and het, John Sheppard/Rodney McKay, Cameron Mitchell/Jennifer Keller, Ronon Dex/Teyla Emmagan, ca. 17,300 words) and Iron and Steel (slash, John Sheppard/Rodney McKay, Cameron Mitchell, ca. 57,300 words). (the whole series also on Wraithbait as "Scruffy AI")
Snakeheads: A Love Story, by Leah. Slash, Rodney McKay/John Sheppard/OMC. (ca. 17,600 words)
I never really expected to read a John/Rodney/Goa'uld threesome, but this was written by Leah, so of course I gave it a try, and wasn't disappointed. This one was far more fun than you'd expect with this setup. Also more bits in a shared universe at the jaffa-for-hire LJ comm.
Aegis, by Leah and Springwoof. Slash, John Sheppard/Rodney McKay. (ca. 90,700 words)
The ATA gene in this AU is somewhat more common than in canon and doesn't just enable people to interface with Ancient technology, but gives them special abilities. (also with further parts as a series on AO3)
As Lost As You Get, by lilysaid. Slash, John Sheppard/Rodney McKay. (ca. 10,000 words)
This is an Epiphany AU. It is not a radical AU, but expands the episode so that after Rodney and the others arrive to rescue Sheppard not all villagers ascend promptly and the Atlantis team can't escape right away, but remains trapped for a while as well. That way the story gives us a look at how Sheppard has changed and at Ascension in general from Rodney's POV.
In the Zone, by Littera Abactor. Gen, John Sheppard (though there's slash and het implied, Ronon Dex/Teyla Emmagan, John Sheppard/Ronon Dex and John Sheppard/Teyla Emmagan). (ca. 2,000 words)
It's a fusion with the concept of The Dead Zone. Here John Sheppard has been in a coma for seven years and now experiences psychic episodes when he touches people.
Guardians of a rare thing, by Livia Penn. Het, Ronon Dex/Samantha Carter. (ca. 6,200 words)
This goes AU from Return I: Ronon comes to Earth rather than stay in Pegasus. Ireally like this take on Ronon at the SGC, and his perspective of Earth. (also on AO3)
Second Best, by Madison. Slash, John Sheppard/Rodney McKay. (ca. 29,800 words)
It's a quantum mirror story in which Rodney, after John's death, tries to fetch a John from another universe, who happens to be a down on his luck gambler. This was a solid action-adventure, with some angst thrown in, as Rodney and the team still miss the "old" Sheppard while getting to know his alternate universe version, while John has to cope with being a replacement. (also on AO3)
Tainted, by Madison. Slash, John Sheppard/Rodney McKay. (ca. 23,000 words)
It's a post-Common Ground story with the premise that the reverse feeding was addictive. I liked this for the angst and the kink, though I found it a bit hard to follow how the timeline of the episodes was shifted around in this AU.
King of Wishful Thinking, by Margie. Slash, John Sheppard/Rodney McKay. (ca. 19,890 words)
It's a fusion with the movie Pretty Woman, with John Sheppard as the hooker. I have a soft spot for that trope/movie, so this was a fun and happy making story for me.
The Fall of the House of Sheppard, by Martha. Slash, Rodney McKay/John Sheppard, Rodney McKay/other. (40,150 words)
This horror AU, in which Rodney accompanies John to Earth during Outcast, was just somewhat creepy at first but also funny, and I was lulled into a false sense of security. Then the creepiness and violence got worse and worse, turning it into genuinely scary horror. A great story overall, that ties horror to the SGA SF elements neatly. (also on AO3)
The Little Sister, by Martha. Slash, Rodney McKay/John Sheppard. (ca. 53,200 words)
I like film noir AUs, and ever since Vegas I like seeing Sheppard as down on his luck detective even more, but what makes this AU great is that the alternate reality is still based on Stargate. The setup is really intriguing, and I like that in it the Goa'uld were smarter in their take over of earth, smart enough that the majority doesn't even think of them as bad guys.
Raiders of the Seven Systems, by Martha Wilson. Gen. (ca. 33,250 words)
It's a space pirate AU, with a very cool premise for the Pegasus cultures, and lots of action and suspense. It hooked me right from the start. (also on AO3)
Retrograde and its sequel Recovery, by Martha Wilson. Gen. (ca. 107,000 words)
It's a crossover with SG-1, and explores how reconnecting with Earth might have gone had the Atlantis expedition been cut off for three years, and SG-1 is just a little bit later than the NID besides. (also on AO3)
Deprivation, by mikes_grrl. Slash, John Sheppard/Rodney McKay. (ca. 9,300 words)
This is a Conversion AU where John doesn't recover completely. As everyone knows I have a really soft spot for Bug!John, and this is a good one of the genre, with nice alien details.
Fair, by Minnow. Slash, Rodney McKay/John Sheppard. (ca. 18,500 words)
This is a delightful AU that takes the premise of fairy!John seriously and makes it fit with the Stargate universe , even though the story has plenty of humor too.
Seven Ways John Sheppard Goes Home, by Minnow. Gen and het, John Sheppard/Elizabeth Weir.
This was written during season one and like the title says it explores different homecoming scenarios for John and the expedition at different times in the future, so you could also see it as more of a futurefic than true AUs, however I think the "what if?" questions it poses make it fit with AUs just as well.
Out into the real world, by Mithreon. Slash, John Sheppard/Rodney McKay. (ca. 21,000 words)
It's a fusion of the SGA characters with The Matrix. I didn't quite get all of The Matrix context, because I've only seen the first movie, and I think this takes place in the future after the third or something, but I could follow it well enough.
Dreams Beneath Our Feet, by Neevebrody. Gen, team. (ca. 9,500 words)
This is an expansion of one of the scenarios from Sholio's Five ways they weren't pirates, which I recced previously. Ronon is captain of a space pirate ship and rescues Teyla and Rodney who managed to escape the Genii. I love this as possible background, and that we get an action-adventure in the an AU Pegasus galaxy. (also on AO3)
Good Guys Don't Always Wear White, by Nel. Slash, John Sheppard/Rodney McKay. (ca. 31,000 words)
This is a fusion with the first X-Men movie. I liked how the mutant powers were distributed among the SGA characters and their histories adapted (casting Michael as Magneto was especially awesome), and it was a good action adventure, that changed enough from the movie to keep the plot interesting too.
Counterpoint, by Nestra. Slash, John Sheppard/Rodney McKay. (ca. 5,475 words)
Another response to the Harlequin Challenge. In this one Rodney teaches music theory and composition, John was court-martialed and takes the job as Rodney's assistant after he's released. It is expanded into a series.
Hands-On Science, by Nindulgence. Gen, John Sheppard, Rodney McKay. (ca. 4,600 words)
John and Rodney first meet in the Toronto Science Center, while John is on a high school trip.
The Protection Racket, by Pares. Slash, John Sheppard/Rodney McKay. (ca. 14,000 words)
This story is great comedy, and made me laugh a lot. Things are set in motion when Jack surprises Rodney as he plays strip poker with Sam, causing Rodney to flee, freak out, and fear for his life, and then to hire John as his bodyguard to protect him from Jack. Only professional bodyguards are harder to find on short notice than Rodney had hoped, so he hires John based on an ad in miscellaneous "Any Job. Sliding scale." Hilarious hijinks ensue.
I Believe in Wishful Thinking, by Pentapus. Gen, John Sheppard, Rodney McKay. (ca. 22,400 words)
I haven't watched the movie that was the prompt for this AU (i.e. "Theodora Goes Wild"), but the story is a great comedy, following Rodney's exploits as he tries to track down the author of an anonymously published math article for the Stargate program in a small town, and runs into the war veteran John Sheppard.
Mercy of the Fallen, by Perryvic and Zaganthi. Slash, Rodney McKay/John Sheppard/Carson Beckett (ca. 102,000 words)
Another magic AU, this time with Sheppard as warlock (there are other magical powers as well). I enjoyed this one because the mix of supernatural elements with the Stargate-kind of pseudoscience worked really well for me, and I liked the action too. (also on AO3)
Converging, by Purna. Slash, John Sheppard/Rodney McKay. (ca. 27,000 words)
It's starts out with John as a lifeguard rescuing Rodney, but this isn't an AU just transplanting the characters into different professions, but branchess off from SGA canon pre-series as becomes clear during the story. (also on AO3)
Any Sufficiently Advanced Technology, by Quasar273. Slash, Rodney McKay/John Sheppard. (ca. 24,100 words)
It's a magic AU, and I really liked how the magic works here, and how it was mixed with science and Stargate mythology bits. (also on AO3)
Four Wars John Sheppard Never Fought (And One He Has), by randomeliza. Gen.
A look at Sheppard as he might have been in different wars, the Revolutionary War, the Civil War, World War II, Vietnam, and finally against the Wraith.
Harvest Festival, by Ras Elased. Slash, Rodney McKay/John Sheppard. (ca. 6,800 words)
This is a cool twist on the "AMTDI because of some backward fertility ritual" cliche, because in this AU the expedition members are Pegasus natives, and Rodney is a disgruntled priest, who's annoyed with the tradition of fertility rituals he doesn't believe in. (also on AO3)
The Hard Prayer, by Rheanna. Slash, Rodney McKay/John Sheppard. (ca. 30,500 words)
You probably have already read this, because everyone and their cat has recced this one, but it is a great apocafic. A plague wipes out most of humanity, and I like this story for showing how surviving the apocalypse damaged them.
The One Where They're Antiglobalization Protestors, by sapote3. Slash, Rodney McKay/John Sheppard, team. (ca. 8,200 words)
Besides being biased in favor of this setting for meta reasons, I liked that the whole team was brought into this AU in a convincing way, and the vivid descriptions and worldbuilding. (also on AO3)
After Such Knowledge, by Sarah T. Het, Michael/Teyla Emmagan. (ca. 7,500 words)
This is an AU of Michael's storyline, with the premise that Michael chose to remain human because Teyla was more honest with him. (also on AO3)
Cross into the blue, by Sarah T. Gen. (ca. 2,000 words)
This is one of those borderline cases between crossover and AU. It meshes SGA with Temeraire, that is John is an aviator with a dragon like from the Temeraire series rather than a pilot. The idea is awesome, and it's enough of an SGA AU in addition to being a crossover that it fits on this recs page.
Diplomatic Immunity, by Sarah T. Het, John Sheppard/Teyla Emmagan. (ca. 4,500 words)
I don't want to spoil this, but it is a creepy and disturbing AU premise in which the Athos the expedition encounters is quite different. But it's disturbing in a good way. Also check out this Untitled Snippet in the same universe (John/Teyla, Teyla/Michael, ca. 2,185 words). (also on AO3)
If not by faith, then by the sword: five happy endings for Teyla and Michael, by Sarah T. Het, Teyla Emmagan/Michael. (ca. 9,500 words)
These AU scenarios for Teyla and Michael were all cool possibilities, though they did not actually all match my own definition of "happy". I especially liked the fourth AU scenario which was a role-reversal. (also on AO3)
In a Grain of Sand, by Sarah T. Gen, John Sheppard. (ca. 540 words)
This is very short and I don't want to spoil it, but it's a cool, twisted premise, and posted as part of the "Skeevy Ancients" flashfic challenge for a reason. (also on AO3)
Six crooked highways, by Sarah T. Het, John Sheppard/Teyla Emmagan. (ca. 2,000 words)
In this AU after Conversion John retained some Wraith-like characteristics and left Atlantis.
The way we look to a distant constellation, by Sarah T. Gen, though with some Sheppard/Wraith non-con. (ca. 3,200 words)
This story takes an alternate route for Vegas!John's encounter with the Wraith. (also on AO3)
when I came I was a stranger, by Sarah T. Het, John Sheppard/Teyla Emmagan. (ca. 12,000 words)
Another Vegas AU (what can I say, I like them a lot), this one closer to canon events in that it is an episode tag. I enjoyed Vegas!John's POV here. (also on AO3)
you already know how this will end, by Sarah T. Het, John/Teyla, Teyla/Michael, Teyla/Kanaan. (ca. 15,000 words)
This is a sequel to Sequelae by The Spike which I have previously recced. And I really like this hopeful resolution to that story. (also on AO3)
Reversals, by Sealie. Gen. (ca. 750 words)
I love stories in which a Pegasus expedition for Atlantis is mounted, and Atlantis then belongs to the Pegasus peoples rather than Earth finding it first. The only downside of this story is that it sets this up, but isn't actually an epic with this premise.
Wide Open Ocean, by Setissma. Slash, John Sheppard/Rodney McKay. (ca. 10,600 words)
John and Rodney work at an aquarium, and I don't actually remember many more specifics, except that it was a nice, entertaining romance story. (also on the Ebook Library)
No Refunds or Exchanges by shalott. Slash, John Sheppard/Rodney McKay. (ca. 11,000 words)
Everybody has already read (and recced) this cool Harlequin challenge response, but it is really great so I'm going to rec it it anyway. Rodney brings John to Atlantis as his mail-order bride.
The Dark Side, by shalott. Slash, John Sheppard/Rodney McKay. (ca. 7,450 words).
This is a fusion with Star Wars. Rodney is a Jedi, John a Sith, though both are a bit unconventional. This story has lot of great funny moments, and it's surprisingly non-angsty for a Jedi/Sith pairing, yet their respective backstories that we find out over the course of the story still make a lot of sense. (also on AO3)
A Clear and Different Light, by Sholio and Naye. Slash, Rodney McKay/John Sheppard. (ca. 88,000 words)
I liked how fantasy and magic were mixed with the SGA mythology here, the plot had me hooked, and this version of Wraith was truly creepy as well. (also on AO3
Five Ways They Weren't Pirates (or: Scenes from Five SGA Pirate AUs), by Sholio. Gen, Het, Slash, team, John Sheppard/Rodney McKay, Rodney McKay/Teyla Emmagan. (ca. 6,000 words)
So I'm not actually all that fond of pirates, and I am a bit frustrated with "five things" stories that kind of tease you with cool AU possibilities, and make you want to learn the whole story behind them, but the snippet is far too short. Still, the scenarios for various kinds of pirates were cool, and made me want to know more, in particular was there no way I could resist a Steampunk AU with them as air pirates.
The Great Pegasus Train Robbery, by Sholio. Gen, team. (ca. 10,500 words)
This humor story casts the team as train robbers in the Old West, and they aren't very good at being bandits, but their efforts are very entertaining.
Knights Errant, by Sholio. Gen. (ca. 5,300 words)
So this is a Knight Rider fusion, with Rodney as the car, John as the driver. And okay, the story doesn't really have much of a plot beyond the setup of John meeting the car, but well, I think the scenario is awesome. (Don't judge me, okay? I liked the series as a kid...)
In Remembrance Bear, by Siriaeve. Gen, John Sheppard, Rodney McKay, Teyla Emmagan. (ca. 1,900 words)
It's a fusion placing John and the others in the Firefly universe.
Truth, Justice and Rodney McKay (ca. 6,800 words), and its sequels Instinct (ca. 650 words) and Inheritances (ca. 1,500 words), by Siriaeve. Slash, John Sheppard/Rodney McKay.
It's a fusion with Superman. John is an Alteran not a Kryptonian, but has Superman's powers, and Rodney is cast as Lois Lane.
The Last Hail Mary You'll Ever Need, by Sly Bone (chase_acow). Slash, Rodney McKay/John Sheppard, Ronon Dex. (ca. 9,000 words)
This is a fun AU in which John Sheppard and Ronon Dex are space pirates and kidnap Rodney McKay. I really liked that here was some backstory given how Sheppard could have ended up as a space pirate while branching off from the SG universe rather than just transplanting him. I missed Teyla in this AU, though. (also on AO3)
Strange Aeon, by Slybrarian. Slash, Sheppard/Mitchell, Sheppard/Lorne. WIP (ca. 110,000 words so far)
How could anyone resist a mix of Lovecraftian space monsters and with Stargate? The series is still a WIP, and I'm really enjoy how this is subtly different from canon, and the world building and hints of mythology so far have me hooked. And I like Cam in Atlantis. (series also on AO3)
The Best Things in Life Are Free, by Smittywing. Slash and het, John Sheppard/Rodney McKay, John Sheppard/Teyla Emmagan, Rodney McKay/Laura Cadman, John Sheppard/Elizabeth Weir.
It's a high school AU. Rodney wants to be cool, so he pays the popular football player John to be his friend for a month, to hang out with him, and teach him how to be more popular. The story is very funny and sweet, and though of course there's some teenage angst it's not overdone, but very believable.
You're a Good Man, John Sheppard, by Smittywing. Gen, John Sheppard, Rodney McKay, Acastus Kolya. (ca. 3,700 words)
John Sheppard is a fighter pilot during the first World War, Rodney is his mechanic and Kolya the Red Baron. Since it is inspired by a Snoopy Christmas special this AU isn't a gritty war story, but it is a very neat and fun idea. Also, the Sheppard-Snoopy association is a brilliant idea: Not just because of their love for flying, they also are both reading War and Peace in their canons at a slow pace, and even the Rodney-Woodstock connection for their respective best friends has several points in its favor, what with both Woodstock and Rodney being unable to fly in a straight line, both liking ice hockey too... (though I can't see Rodney working as John's secretary).
Bright Wings and it's sequel Bright City on Dark Waters, by Snarkydame. Gen. (ca. 7,000 words and 25,000 words)
In this AU Pegasus cultures are squatting in Atlantis, rather than it lying abandoned. It goes further AU than that because the expedition members are among the residents too, with the team running a salvaging operation looking for bits of Ancient tech in the older, submerged parts of the city, but the story still mixes in enough elements from canon Pegasus cultures and Ancient and Atlantis tech that the scenario isn't just some generic fantasy type of city.
A Rough Road Leads to the Stars, by Sonadorita (Freyja). Slash and het, John Sheppard/Rodney McKay, Ronon Dex/Teyla Emmagan. (ca. 7,200 words)
It's an SGA version of the Apollo 13 mission, called Atlantis 13 here: Sheppard, Ronon and Teyla are the crew and Rodney coaches them from the ground. I found the choice to set it in 1967 instead of in the year of the actual mission a bit odd, but apparently the prompt it was written for asked for the 1960s, hence the random seeming timeline shift. But I enjoyed it otherwise.
Ascension, by Soraya. Slash, John Sheppard/Rodney McKay. (ca. 11,750 words)
This Star Wars fusion with John and Rodney as Sith was simply a lot of fun to read, and how could you not like them plotting to take over the galaxy together after their attempts to assassinate each other failed?
Blue, by Sorrel. Slash, Rodney McKay/John Sheppard/Ronon Dex. WIP
And yet another post-Conversion Bug!John AU (what can I say, I like the genre), also Atlantis is cut off from Earth for a while, which is another trope I like. This story is older, only somehow I missed reading it before, and still a WIP that unfortunately hasn't been updated in a while, but the parts stand well enough on their own.
Last Will and Testament, by Speranza. Slash, John Sheppard/Rodney McKay. (ca. 23,200 words)
This is another Harlequin Challenge story. To reveal the twist would spoil the story, but it has a very cool set up, and I love that there's action (that is a road trip to protect an alien artifact) mixed with the relationship plot. (also on AO3)
Left to Fend (ca. 6,800 words), by Springwoof and its sequel The Body Holographic (ca. 68,100 words) by Leah and Springwoof. Gen, the sequel is slash, John Sheppard/Rodney McKay.
I guess you could see this as futurefic, rather than as an AU, but considering that the story takes things into a direction that the show itself is extremely unlikely to ever go, I think it's justifiable to rec it as an AU. This Atlantis has lost contact with Earth again (after the Daedalus reestablished it) for about eleven years, because of trouble the SGC had with aliens, presumably the Ori, in the Milky Way, the Stargate becoming public and the resulting political upheaval. Eventually Earth manages to send a ship again, though we get hints (from changes in organization names and the crew on board and such, that the power structure on earth has changed even though Earth managed to survive the conflict still in human control). Meanwhile Atlantis flourished in its way, but not without costs and things are shockingly different for the contingent from Earth who came to recall the expedition. After reading the first story I was curious about how they could have gotten to this point, but I don't think it would have really worked on its own for me, because there wasn't enough of an explanation. However the sequel expands on that beautifully and gives plenty of background and motivation, including fascinating alien cultures from Pegasus who became Atlantis' allies and how they eventually merge together into something new. It's somewhat non-linear, which I often don't care for much, but fairly clear and easy to follow, and it works to make the threads reveal themselves and come together to great effect. (series also on AO3)
City on the Edge of Forever by synecdochic. Gen, Elizabeth Weir, John Sheppard, Rodney McKay, Aiden Ford. (ca. 6,650 words)
I have no idea why I haven't recced this previously, since I first read it some time ago, but recently I reread it, and noticed that it wasn't on my AU recs page. So it's quite likely you've already read it as well, but if not, it's an AU retelling of the pilot Rising, close to canon but with a more cunning expedition, who come prepared for the worst, and make smarter, more tactical decisions. It's also a cool take on how Elizabeth could have been given more room as an expedition leader.
A Supermarket in California, by taffetablue. Slash, John Sheppard/Rodney McKay. (ca. 7,500 words)
AUs without the Stargate have a harder time to hold my interest, because the SG mythology is so much a part of why I like the series in the first place, but this one is lovely, and the atmosphere and detail sucked me right in. John left the Airforce and Antarctica when he inherited a grocery store near Berkley of all things. Then he meets Rodney who teaches physics there.
The Lonely Sea, by Tarlan. Slash, John Sheppard/Rodney McKay, Jack O'Neill. (ca. 26,500 words)
This is a fusion between the Stargate universe (both SGA and SG-1) and Waterworld, i.e. an Ori attack caused the polar caps to melt. I loved the worldbuilding and the way the two were merged. I cared a bit less about the John/Rodney romance relationship here, but the worldbuilding and rather cool action-adventure plot made more than up for it.
Little By Little To the Truth; or a Narrative of the Atlantis Expedition, by Telesilla. Slash, Rodney McKay/John Sheppard. (ca. 5,800 words)
This is a Steampunk!SGA AU, and beyond the inherent coolness of that, I also really enjoyed the detail and glimpses of their backstories we got here.
Where the Brave Dare Not Go, by Telesilla. Slash, John Sheppard/Rodney McKay. (ca. 18,500 words)
It's of course no secret that I love were-animal stories in general but this one is awesome. I liked the sense of hinted backstories in the AU for the characters, and that the universe seems larger than what's in the story. And I liked that the Were mythology of this universe wasn't magical or really supernatural(at least not from what we learn of it), but seemed almost mundane (in a good way) in the way the society deals with this. (also on AO3)
Unidentified, by The Drifter. Slash Rodney McKay/John Sheppard. (ca. 30,000 words)
Everybody recced this already, but it a really good present-day (no Stargate) amnesia AU, in which Rodney looses his memory suddenly without explanation, and we see him (re-)discovering and to some extent redefining himself and his relationships to friends and family through Sheppard's POV.
Sequelae, by The Spike. Gen, John Sheppard, Rodney McKay, Jennifer Keller. (ca. 26,000 words)
It's a futurefic that goes AU during Adrift, though the past of how Atlantis was lost and the cause of the rift in John and Rodney's friendship is only gradually revealed, as John suddenly shows up at Rodney's doorstep, having a retrovirus relapse.
Needs Salt, by Thetruebard. Gen. (ca. 2,650 words)
In this fusion the SGA team is put into the Avatar the Last Airbender universe in Aang's and his friends' place. This is a lot of fun and it has cute art by Pentapus.
Astonishing Persistence Of Memory: Past Time, by Tielan. Het, John Sheppard/Teyla Emmagan, John Sheppard/OFC. (66,779 words)
In this AU events in Common Ground happen a bit differently, which leads to an amnesiac!Sheppard. I enjoyed to gradually discover what happened and why John lost his memory as John rediscovers himself, and pieces things together as an outsider to his life but also familiar with it. I liked his relationship with the OFC and the UST with Teyla. (also on AO3)
Fly The Stars, by Tielan. Gen, Teyla Emmagan, Ronon Dex, some John Sheppard. (ca. 8,000 words)
This is a very cool fusion with the Firefly universe, with a focus on Ronon and Teyla, that made the SGA characters fit seamlessly in the other universe. (also on AO3)
Living With It, by Tielan. Gen, John Sheppard, Samantha Carter, Jack O'Neill. (ca. 3,730 words)
This AU has Bug!John (which I love), however not as the aftermath of Conversion, but because it fuses SGA with the Marvel mutant concept.
Nexus, by Tielan. Het, John Sheppard/Teyla Emmagan. (ca. 4,300 words)
I like John/Teyla and I like post-Conversion Bug!John, so really this story is an ideal combination. The author labeled it as "porn with a little plot" but the AU worldbuilding still comes through nicely. (also on AO3)
Pegasus Ascendant (part two, three, four), by Tielan. Gen, Teyla Emmagan, John Sheppard. WIP
Pegasus is without Wraith and various Pegasus people share control over Atlantis as the Earth expedition makes contact. I find the premise here very cool, and am glad that it grew into a WIP from the initial flash fic one-shot. (I linked all the parts because last I checked they were not interlinked from the first).
To Serve A Queen, by Tielan. Het, Ronon Dex/Elizabeth Weir, John Sheppard/Teyla Emmagan. (ca. 52,850 words)
This story is a response to the Harlequin challenge and a fusion with Anne Bishop's Black Jewel's universe. I'm not familiar with the books but still enjoyed it as a fantasy story standing on its own. It's a fantasy world with magic and hierarchical castes based on the strength of magic a person wields which is measured in the colors of jewel that are utilized in the spells. Ronon ended up as a slave after his former land Sateda lost a war and Elizabeth, the Queen of the Atlantean court, buys Ronon during a visit to a neighboring court to free him from slavery. Meanwhile Atlantis has also trouble with the Genii and their court. The story isn't very close to SGA, though the characters are about as recognizable as they could be considering that the universe is so different in its setup than canon, but it's definitely a lot of fun to read. Since I first read it it has expanded into a series: Black Jewels Atlantis.
Angels in the Architecture, by Tigerlady. Gen. (ca. 8,300 words)
What if John didn't just have the Ancient gene but was a descended Ancient without knowing it? (needs an AO3 account to read)
String Theory, A Concerto for Violin in D Minor, by Toft. Slash, John Sheppard/Rodney McKay. (ca. 11,500 words)
Rodney is a composer/conductor, John plays the violin, other characters have minor appearances as musicians too. I'm completely clueless about music, but still this one drew me in and even made their music and performance meaningful for me.
The Theory of Acquired Characters, by toomuchplor. Slash, Rodney McKay/John Sheppard, Ronon Dex. (ca. 8,400 words)
In this college AU Rodney is posing as a student to approach John, who's a professor, with the goal to recruit him for the Stargate program and Atlantis without revealing too much too soon. It is apparently loosely based on a movie I'm unfamiliar with and quite funny, especially once Ronon shows up as Rodney's backup.
DADT, Damyata, Dayadhvam, by Trinityofone. Slash, John Sheppard/Rodney McKay. (ca. 8,600 words)
The US government takes its DADT policy a step further and enforces it with an implanted chip.
Irony (ca. 2,600 words) and its companion piece The Numbers (ca. 3,200 words), by Trinityofone. Gen, John Sheppard, Rodney McKay, Samantha Carter
A look at possible backstories for the John and Rodney from the (canonical) alternate reality introduced in the episode McKay and Mrs. Miller.
Mirror Dance, by Trinityofone. Slash, John Sheppard/Rodney McKay. (ca. 45,000 words)
I guess technically this one could count as not-AU because they meet their canon universe counterparts later on in the story through a quantum mirror, so it's more along the line of multiverse fic, but most of this is about an SGA universe in which the gene therapy Rodney underwent had the side effect to transform his body to look like a twin to Sheppard's, and it was a lot of fun to read, with some angst as well.
Tannhauser Gate, by Trinityofone. Slash, John Sheppard/Rodney McKay. (ca. 2,900 words)
John in this AU isn't who he thought he was. The premise is somewhat dark and chilling, but a cool idea.
trinityofone. Gen. (ca. 3,700 words)
It's a fusion with the X-Men (movie) universe. The members of the Atlantis team are all mutants.
Mona Lisa Box, by Tzzz. Slash, Rodney McKay/John Sheppard. (ca. 14,000 words)
This is a fusion between Terminator: The Sarah Conor Chronicles and SGA, and it is a rather creepy love story, with a great twist on the origin of Skynet. I was a bit bothered by the implications the ending had for Rodney's characterization (I don't want to spoil it by being more specific), but apart from that I enjoyed it. (also on AO3)
Where the Ways Divide (971 words) and its sequels In the Nights When I am Lone (2,768 words), To the Wide Outposts (ca. 7,490 words) and The Known From the Unknown (ca. 12,000 words), by Vain_glorious. Gen, John Sheppard, Ronon Dex.
The first is very short, but has still an interesting scenario: It's a role reversal story in which Sheppard is a runner and found by Ronon and his Satedan squad. The sequels explore some more how Sheppard might fare on Sateda.
The Year of Jubilee, by Vain_glorious. Gen, Ronon Dex, John Sheppard. (ca. 20,750 words)
Ronon never joins the expedition because the IOA objected, but helps to fight the Wraith on his own by trading weapons he builds from a base in the ruined Sateda. He crosses paths with them again when he rescues Sheppard from slavery by buying him, and tries to return him to Atlantis, and things go kind of downhill from there. Part of why I enjoyed this is that I have a slavefic as well as a humiliation and mindcontrol kink, all of which are quite prominent here even though it is a gen story and Ronon doesn't want Sheppard humiliated or enslaved. So I think if either of those squicks you, you might want to skip this, though probably the story will also work for you if you just like h/c and Sheppard whumping.
Thule-Gesellschaft, by Valderys. Slash, John Sheppard/Rodney McKay. (ca. 7,600 words) This look at how the alternate universe from the episode McKay & Mrs. Miller might be was creepy and kind of depressing, but full of cool wordbuilding too. It's expanded into a series: Fascist Mensaverse.
Liminal, by Viva Gloria. Slash, John Sheppard/Rodney McKay. (ca. 56,500 words)
Elizabeth is building "Atlantis" as a community on earth, in the post WWII England. I liked the atmosphere of this story, and that despite the setting it is not an AU without the Stargate mythology, things just come together differently. (also on AO3)
Black Helicopters at Dawn (ca. 64,000 words), its sequels Wrong End of the Rescue (ca. 7,000 words) and Black Mountainside (ca. 66,000 words), as well as the rest of the Black Helicopters series (on AO3), by Whizzy. Slash, Rodney McKay/John Sheppard.
Rodney has annoyed the US military too much to become a real part of the SGC, and now tries to prove the existence of aliens the hard way. Meanwhile Sheppard is part of the SGC and crashed an alien craft in a test flight in the Canadian wilderness, and Rodney catches his distress signal. Things unfold from there.
Almost All Grown Up, by Xparrot. Gen, team. (ca. 5,900 words)
I really like AUs with John as a Pegasus native, and making John a Genii, but tell the story from Teyla's Athosian POV, when we as readers know there is more to the Genii, was a narrative ploy I really enjoyed. (also on AO3)
Blue Colorado Skies, by Xparrot. Gen. (ca. 11,400 words)
This is a steampunk western AU. Rodney is an inventor, Sheppard the son of a ruthless railway robber baron, who's trying to get away from his family, which is just a cool scenario all around. (also on AO3)