♥ = absolute fave
Accident Prone by Lady Ra: Something goes wrong during one of John’s missions with his new Stargate team. Set during The Return part 1
♥ The Air That Angels Breathe by Keira Marcos: John has hid his mutation all of his life and then everything changes in an instant.
And Hope by Sihaya Black (beledibabe): While on a mission, John Sheppard discovers a device, but he doesn’t expect what’s inside.
♥ Ashtaroth series Orithain & Rina9294: The real John’s about as far from a hero as you can get. In fact, he’s a demon. 6 parts in series so far, each story complete but series is not, Series Updated:2013-10-02
Breaking Walls by TechnoScribe: Circumstances, and Rodney’s friends, won’t allow him to keep his past a secret anymore. A veritable McKay Whumpathon! Warning! Spoilers. Lots and lots of Spoilers. Ever so slightly AU.
Changes by ChimeraDragon: What if Rodney was infected through his splinter from helping John after Elia attacked him? SGA slash, bug!John, bug!Rodney, McShep
♥ Charming Demeter’s Daughter by sharkie335: Earth cuts off contact with Atlantis. They’re trying to survive, but there’s dissension in the leadership of Atlantis. Plus, someone’s not convinced that all is as it seems. How far will he go?
♥ Clarity by Speranza: Holy shit, Rodney was jerking off to some internet porn or something.
♥ The Conversation by Lady Ra: John overhears a conversation.
♥ Damned If You Do, and Damned If You Don’t by pir8fancier: Post-season, slightly AU take on what happens with the Atlantis team on Earth
♥ Emotional Clockwork by Keira Marcos: At thirty-seven, John Sheppard came to the unfortunate and completely fucked up conclusion that he was in love with Rodney McKay. McKay is fresh out of a relationship and John isn’t interested in ruining their friendship with a rebound thing. Rodney waited for years for John Sheppard to look at him. There had been a time when he would have given anything for his best friend to turn to him and return the foolish, inappropriate love he himself harbored. He thinks he’s moved on but what happens when he turns to John and sees everything he’d ever wanted just waiting for him?
The End Product by melonbutterfly: Weirdly – in hindsight – this is not what clues Rodney in that something is seriously wrong, and later on he wonders what the hell was going on with his brain that the fact that he didn’t like coffee anymore didn’t warrant a trip to the infirmary, stat.
Falling Slowly by melonbutterfly: Things proceed a little different than planned for the Expedition when they find the city of the Ancients already somewhat occupied. By mermaids. Rodney especially doesn’t expect one of those mermaids (mermen?) to fixate on him of all people.
Fat My Dust by Speranza: It turned out that all of life was pretty much like fifth grade.
♥ Friendly by Speranza: “I didn’t know you knew him,” John said. “We were friendly,” Rodney said.
Full Circle by meyari: When Rodney exposed himself to the others to save their lives he expected to be turned in to the SGC. Instead, he got something he hadn’t expected to find ever again.
The Great Doctor McKay by meyari: When the team went to investigate a new planet, I never expected that I’d get kidnapped and turned into a legend. Seriously, all I wanted to do was go home.
♥ Human Nature by Keira Marcos: John faces some hard changes after Atlantis is returned to Pegasus.
Just So Long and Long Enough by busaikko: Dave Sheppard learns more about his brother and gets drawn into a tangle of secrets and truths.
Love Is a Long Long Road by padawanhilary & Telesilla: While shopping, two college students run into each other. Literally.
Love Is a Long Long Road — Ending One by padawanhilary & Telesilla: John and Rodney meet up and then meet up again, but the years haven’t been that easy on them.
Love Is a Long Long Road — Ending Two by padawanhilary & Telesilla: A few weeks after Rodney leaves Stanford, John has things to say and risks to take.
Strangers To Each Other by padawanhilary & Telesilla: As always, John is a man with a plan.
Untitled Long Long Road Snippet by padawanhilary & Telesilla: Rodney’s traded for a pretty awesome sex toy.
Reduce, Reuse, Recycle by padawanhilary & Telesilla: Rodney’s not above repurposing Ancient tech in kinky ways.
Engineers Do It with Precision by padawanhilary & Telesilla: Rodney’s built a little something for John. Or maybe it’s a lot of something.
Remote Control by padawanhilary & Telesilla: Rodney’s not with John, but John’s going to get fucked anyway.
Coming Down Is the Hardest Part by padawanhilary & Telesilla: John gets hurt on the job and Rodney’s not very happy about it.
♥ Loving Rodney by Lady Ra: Atlantis comes to love Rodney, and so does Sheppard: a romantic shmoop fest
♥ A Matter of Death and Life by Rheanna: John’s problems started the day they nearly blew up San Francisco and he didn’t die.
Mistaken Identity by Samantha_kathy: When the team is on Earth, Rodney has the opportunity to speak at a very prestigious symposium. On the day he’s supposed to speak, Teyla gets kidnapped; it doesn’t take the team long to realize the kidnappers think she’s Doctor Meredith R. McKay. Can Teyla play the role of Rodney long enough for the team to find her unharmed?
♥ No Enemy Within by Keira Marcos: John and Rodney face changes in their friendship, Earth’s abandonment of the expedition, and find themselves altered for life when they accept a gift from Atlantis.
Ordinary Life by astolat & Speranza: “So, uh,” Wharton said, with a little nervous cough. “You’re not so much his mathematician as you are his—mathematician.”
Screen Savor by danceswithgary: It was the perfect setup – a little girl with blonde hair, blue eyes, and a pink tutu. What woman could resist?
♥ Sentience series (7 works) by Tarlan: When the eighth chevron locks, Rodney and John take a step into the blue of the Stargate and into the unknown.
♥ Sheppard’s Law by Speranza: “Weird? You don’t know what weird is. Weird is being in a– with the– and the crazy alien–” He stopped, incoherent, hands flailing. “And then your best friend is twelve, and you’re his piano teacher. That–now, you’re talking weird!”
♥ The Situations of War by Keira Marcos: The definition of what a soldier is has changed for the men and women who serve in the Stargate program.
♥ The Slow Slide of Indifference by Ladyholder: When Earth became indifferent to them, Atlantis and the people who loved her looked for ways to make things work. And then Earth tried to change the rules.
♥ An Uncomplicated Choice by Ladyholder: Choosing to stay in Pegasus wasn’t complicated for the people of Atlantis. What happened next? That was where things got interesting.
Tainted by sgamadison: An AU episode tag for S3 ‘Common Ground’. What if all it took was one time for the reverse feeding of the Wraith to be addictive?
Time in a Bottle by astolat: To see a World in a Grain of Sand / And a Heaven in a Wild Flower / Hold Infinity in the palm of your hand / And Eternity in an hour. Stuck in Virtual Reality
Tongues of Men and Angels by Mad_Maudlin: When SG-4 is ambushed offworld, an injured Major John Sheppard must put his trust in a Tok’ra agent named McKay to survive. But what secrets is McKay keeping about his mission, the planet, and his own motives for helping John?
Unforgettable by sgamadison & the_cephalopod: Following the outbreak of kirsan fever during the events in Tabula Rasa, not everyone recovers their memories as expected…
♥ Variations on a Theme of John Sheppard by kisahawklin: A Rodney McKay who’s lost his Sheppard finds an alternate reality drive. We meet him in Vegas!AU and follow his search for other John Sheppards.
♥ Canon in Rodney McKay by kisahawklin: Now that Rodney’s found a Sheppard, what does he do with him?
♥ Interlude by kisahawklin: Teyla the puddlejumper helps the boys get back to the Pegasus galaxy.
♥ Passacaglia by kisahawklin: John and Rodney search for a home.
♥ Unfinished Variations-verse epilogue by kisahawklin: Variations!John and Rodney on the rocky road to deciding to stay in their final home.
♥ What Might Have Been by Keira Marcos: This is an alternate universe series in that Rodney McKay never went to Atlantis, the mission failed within it’s first two years and John Sheppard finds himself back on Earth as the second in command of Stargate Command under the leadership of Major General Jack O’Neill. Characters from the Atlantis series and the original SG1 series will figure prominently in all of the stories. This series also contains a heavy SLASH story line for Sheppard and McKay who meet up (finally) after John returns from Atlantis.
♥ The Home Front by Keira Marcos: PREQUEL (pre-series Sheppard/McKay Pre-slash) John Sheppard comes home
And Then There Was Quark by Keira Marcos: (best read after part 2 of main story)
An Intimate Portrait with Dr. Rodney McKay & Colonel John Sheppard by Iris March by Keira Marcos: (best read before part 5 of main story)
Beautiful Stranger by Keira Marcos: (pre-series Cameron/OMC)
♥ Would You Rather… by penumbria: Based off the “”Trio” Would You Rather? by MeredithKey” writing challenge on Wraithbait. The game of “Would You Rather” that Carter, McKay, and Keller play while trapped in “Trio” goes a little farther. Instead of just asking about celebrities, they start asking about other members of the Atlantis expedition and the SGC. What is up with Carter and O’Neill? Rodney and John? Keller and Ronon? What exactly have these members gotten up to since they joined the Stargate program? Written for Rough Trade 2014 Boot Camp I. All fan fiction is Self-rec
♥ Wraith Killers by Lady Ra: Atlantis ends up with some unexpected new residents