Fandom: Stargate: Atlantis
Characters/Pairings: John Sheppard & Steampunk!Puddlejumper
Media used: pencil, fine liner pen with waterproof indian ink, acrylic paint
Rating/warnings: G
Notes/comments: I did this for the prompt "Victorian steampunk AU" for the SGA fanart fest paintedspires. Admittedly mechanical pterodactyls aren't the most efficient way for a flying machine, Steampunk or otherwise, and not a very likely or even possible path technology would take from an SF standpoint, but this way was much cooler visually than merely changing the puddlejumpers with pipes or gauges or whatever. I mean, they more or less look like flying lunch boxes. Not really realistic technology, but this is Stargate after all, and I'm pretty sure John would think that mechanical, flying dinosaurs were cool.

The original is 30x40cm, so unfortunately I had to scan it in two parts, and you can see a slight line where I merged, because I fail at digital manipulation and didn't know how to make the two parts fit completely seamless.

Preview:
( The image and a higher resolution detail are behind the cut. )

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.

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.

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...)

Bright Wings, by Snarkydame. Gen. (ca. 7,000 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.

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.

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.

AUs

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.

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.

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.

Pegasus Ascendant, by Tielan. Gen, Teyla Emmagan. (ca. 1,830 words)
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, though I wished there was more than this opening. I'm definitely hoping for a sequel.

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crossovers

Only Someone Running, by busaikko. Slash, Rodney McKay/Brendan Dean. (ca. 7,800 words)
Stargate: Atlantis/Thoughtcrimes
This crossover has awesome plot twists, and meshes the two universes well. It is rather sad though.

On the Use of Weapons, by Cofax. Gen, Ellen Harvelle. (ca. 1,600 words)
Supernatural/Terminator: The Sarah Connor Chronicles
In this snippet Ellen observes Sarah, John and Cameron at a gun show, and it gives a great outsider POV of the three.

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Also when I asked on the SGA genrefinder comm for stories with Sheppard as an Ancient or Sheppard ascending, I compiled a list of stories in that genre I had already come across, so I thought I might just as well repost that list on my website as reference. Here's a link collection with stories featuring John Sheppard as Ancient, Ori or Ascended. If you come across any I missed, let me know.

An Unlikely Meeting, by Cofax. Gen, Sam Winchester, Dean Winchester, Chiana, Rygel, John Crichton. (ca. 1,030 words)
Farscape/Supernatural
This just a snippet, more an opening into a universe than a full story, but what we get is such a cool crossover setup that it's worth pointing out regardless.

Nor Hell A Fury, by Lucy Gillam. Gen, Sam Winchester, Dean Winchester, Dennis Guilder, Christine. (ca. 14,800 words)
Stephen King's Christine/Supernatural
I haven't read Christine, but this was still a very enjoyable casefile type of story with neat twists in the the car's background. So if you like to read about the Winchesters hunting monsters or evil cars in this case, you should give this a try.

Untaken Roads, by Tassos. Gen, Dean Winchester, John Crichton. (ca. 4,500 words)
Farscape/Stargate: Atlantis/Supernatural
This gives us another glimpse at Crichton as Runner, like in the previous FS/SGA crossover by Tassos that I've also recced. And seeing him interact with Dean is just fun.

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Also, I forgot to c&p one of my SGA AU recs in the recs post yesterday, so I decided to tack it onto this one:

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.

Stargate: Atlantis

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.

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.

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.

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.

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)

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.

Raiders of the Seven Systems, by Martha Wilson. Gen. (ca. 33,250 words)
I've recced this before when it was still a WIP, but I like it so much that I decided to point you in its direction again, now that it is finished. 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.

Ascension, by Soraya. Slash, John Sheppard/Rodney McKay. (ca. 11,650 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.

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.

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.

Supernatural

Five Families John Winchester Never Had, by Cofax. Gen, John Winchester. (ca. 4,500 words)
In this "five things" story I especially liked the last one, a "Mary survived" AU, but the others had interesting premises as well.

The Boy Who Walked On Stilts (part 2), by Kellifer_fic. Gen, Dean Winchester, Sam Winchester, Bobby Singer, Pastor Jim. (ca. 6,640 words)
The premise of this is that John died early, and Sam and Dean are raised separately by Bobby and Pastor Jim for reasons that become clear over the course of the story.

A Heartbeat At My Feet, by Kellifer_fic. Gen, Dean Winchester, Sam Winchester, John, Winchester, Bobby Singer. (ca.7,400 words)
This is a fusion of Supernatural with His Dark Materials, i.e. Sam and Dean have dæmons.

To Catch a Thief, by Lyra Wing. Gen, Sam Winchester, Dean Winchester. (ca. 8,600 words)
A while back Lyra Wing wrote an AU with Sam and Dean as FBI agents (Paradigm Shift), this is the prequel giving the background how they ended up that way. It splits from canon before the season two finale.

So, I'm going to include this in my next AU recs update too, but you should read it right away, 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: Male Enhancement (The Soul and the Company Store Remix), by Leah. Slash, John Sheppard/Rodney McKay, Carson Beckett, Radek Zelenka. (ca. 46,500 words)

Stargate: Atlantis

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.

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.

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.

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.

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.

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.

A Rough Road Leads to the Stars, by Sonadorita. Slash and het, John Sheppard/Rodney McKay, Ronon Dex/Teyla Emmagan. (ca. 7,240 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.

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.

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.

Supernatural

This Wheel's On Fire, by Marin Rusalka. Gen, Dean, Bobby, Sam, Jess. (ca. 27,800 words)
This is a fusion with the movie Ghostrider. I haven't watched that, and don't think familiarity is necessary as the basic explanations of the Ghostrider premise were covered and merged with SPN mythology too. In any case the image of the flaming Impala leaving blazing tire tracks is better than a flaming motorcycle, and I loved Dean's conflicted reaction to being a Ghostrider.

Rain Fall Down, by Nilchance. Gen, Dean, Bobby. (ca. 2,185 words)
It's the third part in Nilchance's series, and I've already recced the previous stories in this universe, but I thought I'd point it out again, in case you missed it, since it's been a while since the last part. This is a rather bleak AU scenario that explores what might have happened had Mike Gunther called Child Protective Services.

DCU

Mobius Paths, by Marcelo. Gen. (ca. 300 words)
This is short, but with a very neat though somewhat creepy premise: What if Alfred Pennyworth was really J'onn?

Stargate: Atlantis

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.

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.

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.

Raiders of the Seven Systems, by Martha Wilson. Gen. (ca. 9,150 words so far) WIP
It's a space pirate AU, with what seems so far like a very cool premise for the Pegasus cultures, and lots of action and suspense. I'm definitely hooked.

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.

Recs page maintenance is a nightmare these days with all the moving, and worse, f-locking of stories. Just between the last update about a month ago and today several stories have been yanked, actually almost as many as I'm adding in this update. :(

Farscape

Unrealized Peacekeeper, by OneEye. Het, John/Gilina, John/Aeryn. (over 175,000 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.

Stargate: Atlantis

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 already posted here) 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.

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.

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.

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.

Out into the real world, by Mithreon. Slash, John Sheppard/Rodney McKay. (ca. 20,000 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.

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.

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.

Supernatural

Clangs, by Vehemently. Gen, Sam Winchester, Dean Winchester. (ca. 14,800 words)
This was a rather creepy and bleak AU. At first I was confused about what exactly was the premise leading into this (which I won't spoil for you), but then when it became clear, it was even more horrible and hopeless than I expected. But it's a really effective, though tragic, "what if" scenario.

AU recs

Stargate: Atlantis

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.

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.

Harry Potter

The If Sieve, by Cathy (crawfords_lover). Slash, Harry/Draco. (ca. 36,000 words)
Draco goes through potential alternative universes with a pensieve-like device, exploring what would have happened if he (or Harry) made different decisions. It's a cool magical device and the scenarios are HP fandom staples, but handled in an original way, often with not quite the expected outcome.

X-Men Movieverse

Forgotten, by cyndrarae. Slash, Scott/Logan. (ca. 2,450 words)
In this AU Scott survives X3 but has amnesia, and Logan eventually finds him. Also it is hookerfic, so you get two fannish tropes in one, which in this case is definitely a good thing, since they go great together with Scott angst.

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Crossover Recs

Untitled, by siriaeve. Gen, Aiden Ford, Ronon Dex, Rodney McKay, John Sheppard, and the Endless. (ca. 750 words)
Sandman/Stargate: SG-1/Stargate: Atlantis
It's a "Five Things" type story in which SGA and SG-1 characters meet the Endless, and while each vignette is short, they are also gorgeous.

AU recs

Stargate: Atlantis

Mnemonic, or Four Ways John Sheppard Didn't Lose His Mind, by cupidsbow. Slash, Rodney McKay/John Sheppard. (ca. 7,250 words)
I recently reread this story, and was surprised to find that I never recced it. It's four brief AUs all with cool worldbuilding, and all dealing with a different kind of amnesia or altered mind.

Junk Cheap, by devildoll. (ca. 13,000 words)
This AU is just sweet and fun, and John as a junk shop owner was kind of awesome.

Harvest Festival, by ras_fic. 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.

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.

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.

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.

Supernatural

Physiologus, by imogenics. Gen, Sam, Dean. (ca. 5,630 words)
In this AU Sam was pre-med instead of pre-law and tries to find a scientific order in the supernatural phenomena they encounter.

The Sunless Land by lyra_wing. Slash, Sam/Dean, Meg, John. (ca. 11,700 words)
It's kind of rare for me to read Wincest fic, but that they didn't grow up together in this AU made it much easier for me to buy that they'd be attracted to each other, and I have a soft spot for stories in which Sam is kidnapped by the YED and grows up with him and Meg, especially when they are not OTT dark fic, but the demon is still creepy, like in this one.

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crossover recs

Chicago, by ficwriter1966. Gen, Carol Hathaway, Dean, Sam, John. (ca. 4,900 words)
ER/Supernatural
I like outsider viewpoints, so looking at the pre-series Winchesters from Carol Hathaway's POV was really neat.

Knight's Gambit, by killabeez. Slash, Methos/Alva Keel, Duncan/Methos implied. (ca. 4,000 words)
Highlander/Miracles
I admit that I was a little bit lost with the demon plot in this story, because I know very little about Highlander (I've only watched a handful of the first season ages ago and a couple of xovers), but I couldn't resist the allure of Miracles fic. Even missing some of the Highlander context, this was still a very cool x-over premise, not least because Alva as an immortal would not just fit with him knowing all those languages, but explain why that investigation firm of his apparently doesn't really needs to earn money, yet he can still pay his employees.

I'm slowly working through my backlog and updated my AU recs page with the following recs:

Harry Potter

Dudley Dursley and the Hogwarts Letter, by kindkit. Gen, Dudley Dursley, Lily Potter, Harry Potter, James Potter. (ca. 1,940 words.)
This story gives a brief but interesting look at who Dudley might have become had the Dursleys died in a car crash and the Potters survived.

No Way Back, by meri_oddities. Slash, Snape/Harry. (ca. 77,780 words)
It has the same premise as Midnight Blue's Mirror of Maybe, i.e. that Harry gets sent through a magical mirror, gaining experience during an alternate life before coming back, but deals with it differently.

Stargate: Atlantis

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.

Come Back Later, by cottontail. Slash, John Sheppard/Rodney McKay. (ca. 8,800 words)
It's an alternative ending for Tao of Rodney.

The Wrong Side of the Tracks, by gaiaanarchy. 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.

Six crooked highways, by harriet_spy. Het, John Sheppard/Teyla Emmagan. (ca. 2,000 words)
In this AU after Conversion John retained some Wraith-like characteristicsand left Atlantis.

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.

King of Wishful Thinking, by margarks. 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 New Mutants, by mz_bstone. 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.

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.

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 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.

Supernatural

And Everything Nice, by Lyra Wing. Gen, Sam, Dean, OC. (ca. 6,550 words)
I didn't really expect to enjoy an AU in which Sam and Dean have a sister who grows up with them, but gave it a try because I usually trust this author to be entertaining, and this AU really pulled me in, was a great read and I liked the original character.

Gimme Shelter (ca. 7,940 words) and its sequel Paint It Black (ca. 1,330 words), by nilchance. Gen, Sam, Dean, John, Bobby, Missouri. The individual stories are finished, but the universe is still a WIP.
This is a rather bleak AU scenario that explores what might have happened had Mike Gunther called Child Protective Services.

Clay And Paste And Down, by trollprincess. Het, Sam/Jess, John/Mary. (ca. 3,500 words)
It's wingfic, but handles it in a somewhat unusual way, i.e. in this AU Dean was born with wings.