AU recs
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.
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.