Rat Creature's Journal

Doubt, by ALEO. Gen, Don Eppes. (ca. 8,300 words)
Numb3rs/Supernatural
I recced the previous two stories in this series already (Unexplained and Explained), and this one is a good read too. The Supernatural world functions more as a vehicle for Don-whump than as equal crossover partner in this one, but it's not as if I dislike seeing Don hurt, and angst while he adjusts his worldview to the supernatural.

Unwilling Oracle, by Beatrice Otter. Gen, John Crichton, Kira Nerys. (ca. 1,870 words)
Farscape/Star Trek: Deep Space 9
This has a really cool premise meshing the wormhole mythologies.

Angels in the Architecture , by Davincis_girl. (ca. 12,000 words)
Supernatural/Terminator: The Sarah Connor Chronicles
I think the two universes are a great mix, especially when it comes to the various teenage experiences of growing up with pseudo-military training, and here John Connor travels back to 1999 and gets the teenaged Sam and Dean to help him.

Downloaded series, by Ennyousai. Slash and het, Kirk/McCoy, Scotty/Six. WIP (for the series, the stories are finished)
Battlestar Galactica (2003)/Star Trek: Reboot
I'm not familiar with BSG, but the author's notes said it would work if you just knew ST and it did work great as a Star Trek AU.

The Time Has Come to Be Gone, by Jujuberry136. Gen. (ca. 28,950 words)
Criminal Minds/Supernatural
I enjoy stories with the Criminal Minds team meeting and dealing with the Winchesters, and this one is a good action/case story.

The Mutant Problem, by Katt. Gen. (ca. 7,900 words)
Spider-Man/X-Men
This is a very cool multimedia fanfic in the form of a fictional photo essay by Peter Parker.

Pigs in Spaaaaaaaace, by Kayim. (ca. 2,580 words)
Muppets/Star Trek
How could I not love a crossover between Star Trek and Pigs in Space?

For I Have Been a Stranger in a Foreign Land, by Mortigi_tempo. Slash, Kirk/Spock. WIP (ca. 10,000 words so far)
Dune/Star Trek: Reboot
This is a very cool crossover setup. Kirk and Spock get stranded on Arrakis.

Northern Lights, by Se_parsons. Gen. (ca. 9,700 words)
Supernatural/The X-Files
In this one we get an outsider POV of the Winchester family as Mulder and Scully run into them during an investigation.

To Become Immortal, First You Have to Die, by ShadowLoverK. Gen. (ca. 3,200 words)
Highlander/Star Trek: Reboot
Kirk is an immortal and has his first death from an allergic reaction during the movie.

Abnormal Psychology (ca. 1,440 words) and A Sam Adams Moment (ca. 1,500 words), by Siriaeve. Gen, Sweets, John Sheppard.
Bones/Stargate: Atlantis
Sweets working for the SGC is just an awesome and funny premise.

A Thousand Pages, by Tartanshell. Gen, Scott Summers, Matt Murdock. (ca. 6,250 words)
Daredevil/X-Men
In this Matt and Scott were penpals fo a while as teenagers, then meet again as adults.

Harry Potter

House Colours, by Sarka. Slash, Harry Potter/Draco Malfoy. (ca. 12,800 words)
This is a Slytherin!Harry with Gryffindor!Draco AU, and I really enjoyed it, not least because it had a Ron who was first friends with Draco and then Harry, rather than the Ron-bashing that is so depressingly common in Slytherin!Harry stories.

Stargate: Atlantis

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.

The Little Sister, by Martha. Slash, Rodney McKay/John Sheppard. WIP
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.

Strange Aeon, by Slybrarian. Slash, Sheppard/Mitchell, Sheppard/Lorne. WIP (ca. 32,000 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.

To the Wide Outposts (ca. 7,490 words) and The Known From the Unknown (ca. 12,000 words), by Vain_glorious. Gen, Ronon Dex, John Sheppard.
I've recced the other two stories in this series (Where the Ways Divide and In the Nights When I Am Lone) already, but in case you missed these two that have been posted since my last recs update, it doesn't hurt to point the 'verse out again. In it Sheppard has been made a runner by the Wraith and is found and taken in by Ronon and his Satedan squad.

Star Trek: Reboot

Open Up My Eager Eyes, by June. Slash and femslash, Kirk/Spock, Uhura/Gaila. (ca. 15,000 words)
This is a fusion with Pump Up the Volume that was written for reel_startrek. I really enjoyed this, even though I'm not particularly into high school AUs or into making Spock a human/loosing the SF elements in Trek fiction.

Lensflare Lover, by Leftarrow. Het, Pike/Enterprise, Pike/Number One. (ca. 7,300 words)
This has a cool premise in which the spaceships have avatars.

In Truth, by Mint_amaretto. Slash and het, Kirk/McCoy, Spock/Uhura. (ca. 3,570 words)
This is a really creepy, twisted AU, as any mix with the Dollhouse concept (not the series itself, more the basic premise) should be.

The Sky Was Made for Us Tonight, by Waketosleep. Slash, Kirk/Spock. (ca. 5,500 words)
In this AU Vulcans decided to supervise humanity more closely, and Kirk and Spock are delinquent rebels together after meeting in a holding cell and staging a prison break. I enjoyed this scenario a lot.

Supernatural

Untitled SPN Snippet, by Cofax. Gen. (ca. 1,300 words)
I wanted this to be longer and an apocafic epic rather than a snippet, but the world building was still interesting.

Teufelshunde, by July. Gen. WIP
In this AU Sam and Dean grow up with a foster parent after John has been arrested. I really like the OC and the structure with the flashbacks here works for me, even though flashbacks aren't my favorite things.

Rain Falling Down, by Maychorian. Gen, Bobby, Castiel, Jimmy, Dean, John. WIP (the series, individual stories are finished, ca. 20,000 words so far)
In this AU Castiel travels back in time to prevent the apocalyse, but things go wrong and he gets stuck in his host as a kid without his full powers, and lots of angst and h/c ensue.

And Burn the Long-liv'd Phoenix in her Blood, by Tabaqui. Gen. (ca. 6,800 words)
In this AU Mary survives, but they still hunt. I enjoyed the setup and look at their lives.

Seven Moments, by Barrowjane. Gen. (ca. 1,300 words)
Sandman/Star Trek: Reboot
There's just something about other characters meeting the Endless that I really enjoy, and this example of the genre is no exception.

Down The Rabbit Hole, by Bluflamingo. Slash, Colby/Lorne, Colby/Daniel. (ca. 10,000 words)
Numb3rs/Stargate: Atlantis/Stargate: SG-1
I like how this handles the relationships, the complications that come with dating outside of your secret alien conspiracy, and the way the SGC happens to tangle with the FBI here works for me too.

People Who Repair Quantums, or Five Planets The Enterprise Never Visited, by Ignipes. Gen. (ca. 2,800 words)
Star Trek: Reboot/Alien/Discworld/Doctor Who/Dune/Star Wars
I really enjoyed the crossovers for which I was familiar with the sources, also, while I don't know Discworld, the bit where Spock reacts to the flat disc and giant turtle and so on in space was awesome.

Bright White Light, by lilacsigil. Gen. (ca. 35,000 words)
Supernatural/X-Files
This is set during the X-Files episode "Fallen Angel", which I barely remembered, but the story still worked for me. We get the events of the episode but seen from the perspective (and worldview) of young Sam and Dean. I thought it was really cool how one side believes it's all aliens, and the other it's all supernatural and I was wondering what was really going on. And I liked Sam and Dean adventuring.

Exiles, by nwhepcat. Gen, Oz, Sam. WIP
The premise here is that Sam runs into Oz during Mystery Spot. I found this via Cofax and am really enjoying it so far. The parts are all quite short, but it is updated very often.

a fucking space opera (or Six Characters Who Didn't Board the USS Enterprise), by Oxoniensis. Gen. (3,169 words)
Star Trek: Reboot/Harry Potter/Merlin/Stargate Atlantis/Supernatural/Terminator: The Sarah Connor Chronicles
In the best tradition of wacky crossovers, this was simply a lot of fun.

Unexplained, by ALEO. Gen, Don Eppes. (ca. 4,260 words)
Numb3rs/Supernatural
During a serial killer investigation Don runs into the Winchesters. I enjoyed Don's outside POV of Sam and Dean here.

Temporary Alliances, by Cofax. Gen. (ca. 1,930 words)
Stargate: SG-1/Terminator: The Sarah Connor Chronicles
This is short, but has a great Jack POV, as SG-1 runs into a Terminator and Sarah Connor & co.

Connecting Dots & Straight Lines, by This Fish Flies. Slash, John Sheppard/Rodney McKay. (series, ca. 2,500 words so far)
Numb3rs/Stargate: Atlantis
This is mostly fluff with the premise that Sheppard is somehow related to the Eppes, but fun to read.

The Old World, by aesc. Slash, John Sheppard/Rodney McKay, Dean Winchester, Sam Winchester, Castiel. (ca. 10,890 words)
Stargate: Atlantis/Supernatural
They all run across each other on Earth while hunting wraith. This mixed the mythologies of the two shows in a cool way. (As a side note, even though the author labelled it McKay/Sheppard slash, it read gen to me.)

What Keeps The Light, by Eisoj5. Gen, Dan Vasser, Sarah Connor. (ca. 3,000 words)
Journeyman/Terminator: The Sarah Connor Chronicles
I'm a bit ambivalent about this one, because I would have liked to learn so much more of what happened. In a way it is more the start of what could have been an longer story. OTOH a timetravel crossover mixing Journeyman and Dan's involuntary timetravel with the Sarah Connor Chronicles is such a great fit, and I really like the setup here and the possibilities their meeting here opens.

Shotgun, by July. Gen. (ca. 18,000 words)
Friday Night Lights/Supernatural
This is also a bit of an AU, because of course in canon the Winchesters moved around a lot, but it feels more like a crossover than an AU. An the idea of Sam and Dean growing up in Dillon while John still hunts is simply awesome.

Twenty Four Hours, by Morgan32. Gen. (ca. 10,700 words)
Sentinel/Supernatural
This is set pre-series for SPN, and I really enjoyed seeing Sam and Dean as teenagers through Jim an Blair's eyes.

Stargate Atlantis

A new history of Captain John Sheppard, by Anonymous. 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.

Liminal, by Anonymous. 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.

Stargazing, by Anonymous. 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.

Orpheus, by Domenika Marzione. Gen, John Sheppard. (ca. 53,000 words)
This story explores what might have happened had Sheppard been not allowed to return to Atlantis after the Seige.

Supernatural

Rising Storm, by Cofax and Hossgal. Gen. (ca. 11,000 words)
This is a fusion with the Finisterre universe. I haven't read those books, but they made for a cool AU scenario of settlers on a hostile planet with telepathic fauna.

DCU

Shards of Night, by Marcelo. Het, Lois/Clark. (ca. 830 words)
Clark in this story is more alien than in canon. The story is on the scary side, but I actually felt sorry for Clark, because he's still one of the good guys.

The Call, by Marcelo. Gen, Bruce Wayne. (ca. 450 words)
Another short, yet scary DC AU. The author describes it as "DC Comics meets Lovecraft" and I really like the creepy premise for Batman here.

Supernatural

Dromoscope, by Emily Brunson. Gen, Dean Winchester. WIP
It's a fusion with the novel "Jumper". I haven't read that, but still enjoyed the story so far. The premise is that Dean is able to teleport, and keeps this secret from his family.

The Heist, by Starrylizard. Gen.
This last one isn't a fic rec, but an AU vid. It is really fun though. Sam and Dean are bankrobbers.

Stargate: Atlantis

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.

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.

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.

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.

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.

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.

Where the Ways Divide, by Vain_Glorious. Gen, John Sheppard, Ronon Dex. (971 words)
This 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.

Blue Colorado Skies, by X-parrot. 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.


Supernatural

A Thin Chain of Next Moments, by batyatoon and dotfic. Het, Sam/Ava, Dean/OFC, John. (ca. 22,000 words)
In this AU Dean makes a deal with the Crossroads Demon to free John from hell, and gets the standard ten years contract. On the one hand this AU is quite sad, on the other we get to see Dean live for a decade.

Art Therapy, by CaffieneKitty. Gen, Dean. (ca. 1,200 words)
In this AU Dean was the only survivor of the fire. What gives this story a great twist is that it is written from various outsider POVs of report cards and therapy notes.

Appointed Verse, by Irnan. Het, John/Mary. WIP
A Mary-centric AU verse. Mary survives, and she and John become hunters together.

Pathways Verse, by Irnan. Het, John/Mary. (ca. 36,000 words)
This is another Mary-centric AU verse (though Sam and Dean appear too), that gives her an interesting supernatural background of reincarnation and connects her to Samuel Colt as well as Ruby.


Multifandom

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

Pass the Pork-Barrel Salt, by Gwendolyn Grace and Etakyma. Gen, Sam Winchester, Dean Winchester, Josh Lyman, Donna Moss, C.J. Cregg. (ca. 5,000 words)
Supernatural/The West Wing
Josh meets the Winchesters during a "Big Block of Cheese Day". This crossover is simply a lot of fun.

Begotten and Gingerbread, by Nilchance. Gen, Alec, Sam Winchester, Dean Winchester, Boby Singer. WIP
Dark Angel/Supernatural
I'm not actually sure whether this is a series or a WIP, but I find it intriguing so far, because in this crossover the timelines of DA and SPN don't seem to have been messed with to mesh them, but instead Alec somehow ended up in 2008, though neither he nor the Winchesters seem to know the how or why yet.

Travelled on his looks, by Petronelle. Gen, Fraser, Ray K., Dick Grayson, Tim Drake. (ca. 2,200 words)
DC Universe/Due South
I'm not much interested in crossdressing, but Fraser and Ray teaming up with the Batclan here was fun.

Untitled, by Tassosss. Gen, Teyla Emmagan, Aeryn Sun. (ca. 2,840 words)
Farscape/Stargate: Atlantis
Teyla and Aeryn team up for a jailbreak, which is simply a great scenario.

Woman Inflammable, by Vehemently. Gen, John Winchester, Sarah Connor. (ca. 4,660 words)
Supernatural/Terminator: The Sarah Connor Chronicles
I really enjoyed this insight into John at the beginning of his hunting life, and the outsider look at Sarah. And of course John would have the worst luck in that that he picks Sarah Connor & Co to run into early on.

where the grass is green and the girls are pretty (ca. 2,165 words) and its sequel oh, won't you please take me home (ca. 2,700 words), by Vorrothiel. Gen, Ash, John Connor.
Supernatural/Terminator
There's something about crossovers between Supernatural and Terminator that really appeals to me. The universes just go together like hazelnuts and chocolate, IMO. Anyway, this one has the unique premise that Ash used to know John Connor in high school.

Stargate: Atlantis

Any Sufficiently Advanced Technology, by Anonymous. 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.

Little By Little To the Truth; or a Narrative of the Atlantis Expedition, by Anonymous. 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.

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.

Engineering the Fall, by Layton Colt. Slash, Rodney McKay/John Sheppard. (ca. 4,300 words)
This is a sequel to Gods that Slumber, which I have recced before, an AU in which John is an Ancient.

Pegasus Ascendant (part two, three), by Tielan. Gen, Teyla Emmagan, John Sheppard. WIP
The Wraith never subjugated Pegasus, so the Atlantis expedition makes contact with a city that has been settled by various Pegasus cultures and has to try to fit in. I've actually recced this before when the first part was posted as a flashfic on its own, but now it has grown into a longer WIP and I thought it worth pointing out again in case you missed the second and third bit being posted (I linked all the parts because last I checked they were not interlinked from the first).

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.

Supernatural

But Deadly series, by Bella Temple. Gen and het, Sam Winchester, Dean Winchester, Bobby Singer, some Sam/Jess. The individual stories are finished, but the universe is still a WIP.
So far I find the setup of this AU really intriguing. Here John was killed by the YED, Sam and Dean grow up with adoptive parents because Mary left their home right before the demon attacked for a reason that has not been revealed yet, though there are hints, and there is other stuff going on too... anyway, there's three stories so far and the universe has me hooked.

Steam, by Bella Temple. Gen, Sam Winchester, Dean Winchester, some Dean/Steampunk!Impala bonding. (ca. 30,000 words)
In a post-apocalyptic world Sam and Dean try to figure out what happened, to find other survivors and to make the impala run on steampower. I enjoyed the mystery and the plot twists here, and of course a Steampunk!Impala with Dean as its engineer is awesome.

And Won The Soul's Rest, by Concernedlily. Gen, Sam Winchester, Dean Winchester. (ca. 31,000 words)
This is a medieval AU with Sam as a monk and Dean as a mercenary, and the plot parallels to canon with the demon worked very well. As a Big Bang story it also came with art by Glockgal and Reallycorking that complemented the story nicely.

Scheduled for Termination, by Dolimir. Gen, Mary, Dean, Sam. (ca. 20,945 words) This is a fusion between Supernatural and the Terminator universe. Here Mary survived the demon to become a hunter, which in turn equipped Dean to become part of the resistance. Then of course there's the Terminator kind of time travel, so in the end poor Mary has demons after her one son and robots after the other.

Older Than The Days He Had Seen, by Kellifer_fic. Gen, Dean Winchester. (ca. 3,700 words)
This AU is rather sad. It explores how the Winchester family would have been different and yet the same if Sam and Dean had had an older brother.

The Crow on the Cradle, by Kroki_refur. Gen, some Sam/Jess. (ca. 98,200 words)
The starting point here is that one day Sam walks out on Jess, who then searches for him together with John and Dean, and learns about hunting. Not just has this story Jess as a hunter, but Sam is kind of broken in an interesting way that I don't want to spoil too much.

Berserker!verse, by Leonidaslion. Gen, Dean Winchester, John Winchester, Sam Winchester, Bobby Singer, also some het, Dean/Cassie. The individual stories are finished, but the universe is still a WIP.
During Sam's Stanford days Dean has an unfortunate encounter with a berserker (in the context of this universe someone sharing their body with an animal spirit which more or less grants various superpowers), which leads to a wolf spirit choosing Dean as a host. Much angst and complications follow. The series eventually progresses through the first season episodes. (The above link goes to the verse's tag, but you can also go right to the first story Heart of a Wolf, as all following stories are interlinked.)

There is also a rather epic slash continuation of this universe, Fetters of Fenrir (mostly Sam/Dean, ca. 200,300 words), and even though I'm not much into Sam/Dean as a pairing the universe interested me enough to want to read all stories in it. And I enjoyed that novel for the plot which had me hooked, for Dean being hurt in various ways, and also for the supernatural mythology bits about the demons and the berserkers here, even though incest soulbonds are not one of my kinks. However if you are squicked by that pairing, the author's notes mentioned that the regular Berserker!verse will be continued as gen, so you should be able to just skip the slash spin-off novel without being left hanging once the next story of the regular verse gets posted.

Revelations, by Marina Rusalka. Gen, Victor Hendricksen, Dean Winchester, Sam Winchester. (ca. 24,200 words)
Here, Dean is an ATF agent who works with Victor Hendricksen on the serial arson case of the demonkids' ceiling fires. I enjoyed that we were led into this AU through Hendricksen's POV, and how Dean and Sam's backstory was revealed gradually. Also it has great art by Ileliberte.

Daylight Refracted, by Pix. Het, Sam/Jess, Dean. (ca. 7,585 words)
This is a really happy making AU in which Jess comes from a family of hunters, survives the YED's attack, and hunts together with Sam and Dean.

Show me a hero and I'll show you a tragedy, by Unperfectwolf. Gen, Dean Winchester. (ca. 2,575 words)
The premise here is the basic "what if Sam and Dean grew up 'normal'?" that is they haven't been raised by John but by other relatives, though John is alive. What it made it stand out to me was that the reality of the demon and John's hunting of supernatural monsters remains ambiguous throughout.

I just finished reading Lovesrain44's Big Bang story, Phantom Load (gen, Sam and Dean, set present day and pre-series, ca. 54,000 words), and though it kind of gutted me, it's a great story. While the story is gen there are explicit scenes of sexual abuse of a young Dean by an original character, and I think it's one of the most harrowing child abuse stories I've read in fandom. Not because it is particularly extreme or bleak, but because the way the memories are narrated, the details, and the past and the present, and Dean and Sam's POVs are woven together made it very real to me.

Also, even if you don't think you can stomach the story, you should take a look at Xterm's drawing, which is lovely and can stand on it's own as a picture of their childhood, even though looking at it again after reading there are added layers to the artwork.

I've updated my AU recs page, and also split it into subpages, which based on my poll from earlier today seems to be the much favored option over one monster page. I hope I didn't mess up anything when I c&p'ed all the stuff into separate pages, but it looks okay to me. The main URL is the same and continues as an index page to the subpages, so no links to my AU recs page will be broken. That page now also lists the most recent updates, like these update posts, so that people won't have to click further than the main page for the just latest recs.

Stargate: Atlantis

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).

The Difference Engine , by Copperbadge. Slash, Rodney McKay/John Sheppard. (ca. 21,600 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.

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.

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.

Supernatural

Golden Lights Go Dark Tonight, by Pix. Gen, Sam Winchester, Ruby, Dean Winchester. (ca. 5,100 words)
I guess this AU is a take on the old theme of the road to hell being paved with good intentions. DarkSide!Sam is not normally my thing, but this story puts an awesome twist on this. It's a dark AU that sucker punches you with its brilliant premise.

Miles Before I Sleep, by Silverkit. Gen, Sam Winchester (there's a brief Sam/OFC sex scene but no relationship). (ca. 1,860 words)
It's a great, if painful, look at a Sam who decided not to go to Stanford, but to stay with his family.

Nothing Like Billy, by Embroiderama. Het, Ellen Harvelle/Fox Mulder. (ca. 2,622 words)
Supernatural/The X-Files
There isn't much plot beyond the sex in this crossover, but there was enough characterization and a plausible reason for their meeting to not have the story feel arbitrary.

Leapin Lizards, by Gwendolyn Grace. Gen, Sam Winchester, Dean Winchester, Sam Beckett, Al Calavicci. (ca. 18,560 words)
Quantum Leap/Supernatural
Sam Beckett leaps into John Winchester when Dean and Sam were still children. There is a good case story, and Beckett has to deal with finding out that the supernatural is real, and handle two young Winchesters.

With a Bang, by Mink. Gen, Alec, Dean Winchester, Sam Winchester. (ca. 42,000 words)
Dark Angel/Supernatural
This is a good action-adventure, and I liked how the shows' mythologies were meshed, even though I'm not that into the whole breeding cult arc of DA season two. Also Alec, Sam and Dean together are just fun to watch.

Curiosities (ca. 4,045 words) and Stutter (ca. 1,500 words), by Penknife. Slash, Erik Lehnsherr/Charles Xavier, Tom Riddle, Lily Potter, Sirius Black.
Harry Potter/X-Men
Recently Penknife offered to write timestamp fic, and I noticed that I never recced the original crossover for which I requested a timestamp. Anyway, in the first Erik Lehnsherr encounters Tom Riddle in 1950, the timestamp is set during the first Voldemort war/the Marauders era, and both are interesting and well worth reading.

Brothers in Arms, by SylvanWitch. Gen, Dean Winchester, Derek Reese. (ca. 2,440 words)
Supernatural/Terminator: The Sarah Connor Chronicles
Dean runs into Derek while hunting, and somehow these two shows just go together like chocolate and hazelnuts.

What Kind of Day Has It Been?, by Victoria P. Gen, Dean Winchester, Sam Winchester, Kermit and the Muppet Show ensemble. (ca. 3,300 words)
Muppet Show/Supernatural
I love Muppet crossovers (felt rules! *g*), and this one made me laugh a lot.

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.

I updated my crossover recs page.

Take a Long Line, by Derry667. Gen, Dean Winchester, Sam Winchester, Don Eppes, Charlie Eppes, Alan Eppes. (ca. 22,000 words)
Numb3rs/Supernatural
The Winchesters are trying to stop a psychic arsonist at CalSci, which we see through the eyes of the Eppes. I liked how competent Sam and Dean were in this story as well as the the outsider look at them.

Defect, by Kikkimax. Gen, ensemble. (ca. 39,600 words)
Criminal Minds/Supernatural
This is set after the second season finale of Supernatural. While Sam tries to get Dean out of the deal with the demon with the help of Bobby and Ellen, Dean is taken into custody by the FBI and interrogated and evaluated by the BAU team. I really enjoyed the take of the profiler team on Dean, and how they try to make sense of him and revise their opinions without ever actually buying into Dean's supernatural worldview.

Untitled snippet, by Pentapus. Gen. (ca. 230 words)
Highlander/Stargate: Atlantis
This is just a brief snippet, but it is a very neat idea to merge the mythologies of the two shows.

Take Atlantis, by Siegeofangels. Gen. (ca. 800 words)
Muppet Show/Stargate: Atlantis
This is quite short, and doesn't really have a plot beyond "the Muppets visit Atlantis", OTOH having the Muppets on Atlantis is awesome and funny.

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.

I updated my crossover recs page.

Old Country, by Astolat. Slash, Sam/Dean. (ca. 40,600 words)
Harry Potter/Supernatural
I don't read a lot of Wincest, but I think this crossover is a great read even if you prefer gen. It's a lot of fun, humor mixed into the angst and drama, and the merge of the Potterverse with SPN here works great, and I liked the take on goblins and their magic in particular.

Harvester of Eyes, by gwendolyngrace. Gen. (ca. 26,000 words)
Sandman/Supernatural
John Winchester hunts the Corinthian, meanwhile Sam and Dean get lost in the Dreaming. This crossover is a great blend of the two sources.

New Jersey Voodoo, by Rokeon. Gen. (ca. 1,020 words)
House/Stargate: Atlantis
This is short, but really funny. John has a relapse back towards Bug!John, starting with an at first innocuous rash and progressing from there, and House tries to diagnose.

Late Nite at the Sudzy Dudz, by Sarah Ellen. Gen. (ca. 3,500 words)
Supernatural/The X-Files
I have no idea how I could have missed reading this story for so long. This crossover is a lot of fun. I guess you could sum it up as "Mulder and Scully meet the Wincesters in a laundromat and talk about cattle mutilations." but the dialog is awesome and it made me laugh a lot, while still being plausible and in character within both series.

The Curious Incident of the Doc in the Night-time (part 2), by Taz. Gen. (ca. 2,920 words)
Highlander/House
House meets Methos in his morgue and is understandably curious. Snark ensues.

Winchesters at Hogwarts series, by Ignipes. Gen. (so far three stories with ca. 10,400 words)
Harry Potter/Supernatural
In this crossover AU John dies and Sam and Dean are sent to wizard relatives in England, so Dean attends Hogwarts.

And All the World Beneath, by Jenn. Slash, John Sheppard/Dean Winchester, John Sheppard/Rodney McKay. (ca. 67,000 words)
Stargate: Atlantis/Supernatural
This is a very cool and creepy apocafic, meshing Stargate and Supernatural in a way that makes sense for both mythologies.

Agents of Fortune, by Karasu Yurei. Gen, Dean Winchester, Sam Winchester, Alec, Lydecker, Renfro. WIP
Dark Angel/Supernatural
So far this seems to be a basic "let's make these characters meet" crossover, but it has a plot that makes sense and the way the universes are mixed is interesting. It's not exactly the canon universe for Dark Angel in that there was no Pulse, but it still feels more like a crossover than an AU premise. X5-494 is given the mission to kidnap Sam for the Manticore program, so he tries to impersonate Dean.

Bent, by Rachel Martin. Gen, Dean Winchester, Sam Winchester, Ororo Munroe, Scott Summers, Logan. (ca. 12,300 words so far) WIP
Supernatural/X-Men
This is set during the SPN episode Benders. Scott thinks that one of the Winchestes is an out-of-control mutant and goes to search for them to stop the deaths he thinks the Winchesters are responsible for.

I've accumulated enough of these to make a page worthwhile, so I've compiled all my previous crossover recs on a webpage, so that I can fix links and such in one place rather than assorted posts.