McKay/Sheppard thematic fic index >> AU - Quantum Stargate: Alternate realities
2.473 billion to one by
When the Ori destroyed Earth, a secret evacuation had been going on for several months. A few hundred thousand people had been sent through the Stargate into the Pegasus galaxy, settling into new lives on different planets all around.
A SGA Sentinel and Guide by
John is an unbounded Sentinel, Rodney is his destined Guide.
Abscido by
Sateda is a nation standing against the Wraith. Once mighty, they now rely on raids to other worlds to fill their military. On Ra-Yeda, circumstance leads to the capture of two men who may be their downfall.
And Hope by
While on a mission, John Sheppard discovers a device, but he doesn't expect what's inside.
Animalia Sequence by
Pegasus B AU. John and Rodney get turned into penguins.
Architects of Fate by
SGA/SG1 AU crossover based on David Hewlett's TV movie Survivor.
Baby Boom by
"You’re pregnant and you didn’t plan on telling me? You wanted to get rid of it without ever letting me know I could have been a father? Don’t you think this should be my decision, too?"
But Trailing Clouds of Glory, Do We Come by
When Rodney loses Sheppard, he devises a way to get him back.
Candy Floss by
Rodney runs away from the SGC to join the circus, instead of going on the Atlantis mission. Then he meets a handsome motorcycle stunt driver who teaches him that love can conquer fear.
Chance of a lifetime by
Being sent to recruit someone for the Atlantis expedition wasn't Rodney's idea of a good time.
DADT, Damyata, Dayadhvam by
A world where Don't Ask, Don't Tell was taken to the extreme.
Dawn Will Break by
When Atlantis - upon returning to the Pegasus Galaxy from Earth - breaks apart in hyperspace, only John is saved from the debris. The group of Ancients that retrieved him offer him a bargain: Either he helps them make corrections in some universes, where things have gone wrong, or they put him back where he was found. Reluctantly accepting, John embarks on a lonely journey through a multitude of universes until he finally reaches the place he could again call home.
Doctor/Patient Confidence by
Rodney is a medical doctor, John is his amnesiac patient.
Ersatz Void by
Part two. Rodney was left behind by the Atlantis mission. Two years later, by a strange coincidence, he gets to join them, but things have changed a lot
Evil Overlord Sheppard by
Rodney is captured by High Lord John of the Planet Leiath in the Pegasus Galaxy.
Finding Home by
John is a Slave who ends up the property of one Dr Rodney Mckay
Foreshock by
Elemental SGA ficlets. More in the series: To be mud instead of stars; It could move you like a wind; Aftershock; All I can do it hold you tight
Genus by WIP
Rodney and Jeanie are genies. In bottles. Link is to part 6; links to other parts are on the page.
Golden Opportunities by
She thought it was a golden opportunity to show the council her true worth.
Here is the secret that everyone knows by
John stops wearing his uniform on the two thousand and second day after they arrive.
His Bodyguard (series) by WIP
AU where John (and Ronon and Teyla) are bodyguards for one Dr. Rodney McKay. Link is to series page.
How Not to Fly by
Death and life, hope and hopelessness, aren't just for the Pegasus galaxy. Eventually, inevitably, it's going to happen on Earth. John and Rodney, loss and family and what it means to be home.
How There Was A Giant Conspiracy To Kidnap Rodney And Possibly Even Torture Him by
John Sheppard needs to prove his innocence. Unfortunately, he ends up with Rodney McKay in his stolen car. In 4 parts: Part 2; Part 3; Part 4
Lord of the Sea universe by
Originally created by lavvyan in the story Lord of the Sea. Now all stories by her and other authors are available in the jaffa_for_hire community. John is host to the Goa'uld Mer'deth, who's something of an oddity.
Make The Devil Feel Surprise by
In a dark mirror universe of our own, sixteen year old Rodney McKay is brought to Atlantis by the Chief Science Officer, his older sister Jeannie, after their parents die. While Jeannie has no real use for Rodney, Colonel Sheppard does. Now Rodney has to come to terms with the fact that not only is he Sheppard's boy toy, but also that Sheppard is a moody, paranoid sadist.
For his part, John isn't quite sure what to make of Rodney, who is an almost too perfect match for him. Just as he and Rodney carefully start to settle into a complicated relationship, a conspiracy begins to surface, forcing Rodney to take a stand.
Also Jeannie McKay/Ronon.
Mau Loa Means the Time We Have by
Companion piece: Goodnight, Chesty, Wherever You Are. Sequel: Timestamp.
Morale Assignment by
AU in which the the military are basically the lowest of the low, and Rodney chooses John to have sex with. Rodney is only concerned about getting off, but John has feelings for him and gets all angsty.
Mother's Day by
A McShep AU wherein Meredith has always been a girl and John is in love with her now more than ever.
My Favorite Colonel by
AU based on the Cary Grant/Irene Dunne 1940s classic movie, "My Favorite Wife."
N.O.R.W.I.C.H. by
Of course he'd be a dean or something, because he couldn't see, so he couldn't fly. And there Rodney was, in the Air Force and probably doing everything John had wanted to do. Fucker.
Necromancy for the Living by
How does John write a mission report about something no one wants to hear? Missing scene for Auburn's In the City of Seven Walls
No Refunds or Exchanges by
Atlantis head scientist Rodney orders a mail-order bride. He gets ex-military pilot John instead.
Nowhere Land by
About to be ripped apart by the psychic attack of a Wraith Queen, Telepath Rodney McKay does something no-one has ever done before: he reaches out.
Out of the Closet, Into the Fire by
Jack knew things were going to happen when he greeted Daniel with a kiss while they were right in the middle of a hall in the Pentagon.
Pegasus B by
An AU universe with several off-shots. One of them is Daniel/Rodney -> Daniel/Rodney/Sheppard -> Rodney/Sheppard & Jack/Daniel. See the Pegasus B Story Guide.
Plan C, or How Rodney McKay Lost His Wife and Gained a Galaxy by
Billionaire Rodney learns that his soon-to-be ex-wife Sam Carter has a new boyfriend, John Sheppard. And who gets the cat in the divorce?
Second Chance by
Major Sheppard always wondered how his life would have turned out if he had only gone on the expedition to Atlantis instead of returning home at his father's request.
Snakeheads: A Love Story by
Wherein John Sheppard is host to Mer'deth, a brilliant, arrogant, and not-entirely fearsome Goa'uld.
Storm Damage by
Sequels: Five Times Aiden Ford (Almost) Wished He Was on a Different Team, Every Farthing of the Cost, Five Times Meredith McKay Came Out
Teamwork by
John is a math doctor, Rodney is a RCMP Staff Master Sergeant, but they go to Atlantis all the same.
The Air That Angels Breathe by
Mutant!Verse. John has hid his mutation all of his life and then everything changes in an instant.
The Bribe by
Rodney given to John as a slave and they're on their way to Atlantis.
The Crate by (url needed)
Rodney didn't go to Atlantis. Some time later, he gets a crate with a mysterious creature inside...
JOURNAL PURGED. New source req.
The Last Hail Mary You'll Ever Need by
Earth-born John is the captain of an spaceship in the Pegasus Galaxy whose life changes forever the day his second in command, Ronon, captures Atlantis expedition scientist Rodney.
The Providence of Stars by
In the summer of 1942, young Dr. Rodney McKay steps off a train, eager to continue his work on the war effort. Nearly a year later, he's running for his life with Captain John Sheppard.
The Roads Never Lead Where They're Supposed to Go by
John is a botanist, Rodney is not in charge, Summer is still alive.
The Sentinels of Atlantis by
While the main focus of this series is the slash pairing of Sheppard/McKay there are secondary het pairings. The pairings that appear in the series: John Sheppard/Rodney McKay, Cameron Mitchell/Vala Mal Doran, Jennifer Keller/Evan Lorne, Teyla Emmagen/Ronon Dex, Sam Carter/Daniel Jackson, Laura Cadman/Aidan Ford, James Stackhouse/Thomas Markham, and Radek Zelenka/David Parrish.
Sentinel John Sheppard thought he’d spend his life unbonded and then he met Dr. Rodney McKay. The mission to Atlantis is their mutual path and they will gather the strongest, brightest, and best for the mission that will take them to another galaxy.
The Sweep of Easy Wind by
John is a military prisoner under Colonel Caldwell's command. Controlled by Goa'uld technology, he is little more than a slave. Briefly stationed on Atlantis, his ATA gene is discovered by Rodney, who is a force to be reckoned with.
There's No Such Thing as Daniel Jackson by
Implied Sheppard/Holland.
Six months after a devastating attack against Earth, Sheppard gets a promotion and a reassignment to Russia, where he encounters evil aliens, Rodney McKay, SG-1, a possible plot against him -- and a series of unexplained visions.
Through the Noise to the Sea by
John has time to realize that those fingers are webbed and then the involuntary laughter about finding a mermaid interferes with his already questionable grip on breathing, and he passes out.
To Serve And Protect by
John Sheppard/Elizabeth Weir, Rodney McKay/John Sheppard, implied John Sheppard/everybody
Right or wrong, things had always been the way they were, the intelligentsia ruling and the military serving.
Together by Demand by
Rodney's condition to work with the SGC again is to have a military husband of his choice.
Tongues of Men and Angels by
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?
Trust Issues by
Kicked out the airforce, John works for The Trust, but he don't really trusts them. He's looking for a way out of it for himself and Rodney.
Unified Theory Series by
Everett was never drained by the Wraith and kept his position as military commander of Atlantis.
Wear a Rainbow by
In an alternate reality, Captain Richard Holland earned a black mark in Afghanistan, Major John Sheppard lost the sky, and Rodney McKay remembers.
Welcome to Atlantis by
John is a medical doctor trained in emergency medicine. Rodney is an USAF Major.
What Might Have Been Series by
Also past McKay/Quinn, McKay/Mitchell, Sheppard/Holland, Sheppard/Mitchell and present O'Neill/Carter, Dave Sheppard/Keller, Mitchell/OMC, Lam/OMC & OMC/OMC.
What if Rodney didn’t go to Atlantis and the city was lost again? Sheppard turns up as the second command of the SGC under Major General Jack O’Neill and after a year of watching the moody government contractor Dr. Rodney McKay… he decides to make some very personal changes in his life.
What's Love Got To Do With It? by
In this Alternate Universe version of the SGA pilot, Rising, Colonel Sumner is in charge of an expedition which is almost all male and all military. John Sheppard is a military pet - a submissive who has been trained to service others. Sumner decides he has to prove he is trustworthy before letting him go on the expedition, so has Sheppard come to his house to bond with the Marines. Later, he tells O'Neill he accepts Sheppard, but O'Neill has to see for himself first. Once they are in Atlantis, Sheppard is restricted to helping out in the labs, rather than going on missions, so Sumner gives control of him over to Rodney McKay, who is still head scientist on the expedition.
