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2.473 billion to one by darkmoore

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.

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20 September by enviropony

It's just past midnight on 20 September, 2011, in the middle of the northern ocean on New Lantea II.

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A Different Rate of Conversion by Ionaonie WIP

What if Carson couldn't completely cure John from being a bug. More parts here: Part 2. Part 3, Part 4, Part 5,
Part 6, Part 7

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A Growing Connection by Joulez217

(Prompt: Big Bang 2008. John is more Ancient than anyone realizes) With two new growing connections, can John Sheppard cope or will he give in?

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A Knot Better Left Untied by reddwarfer

"Something's wrong with the Stargate. Our Stargate. We can't dial home."

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A Sappy Country Love Song by allwhowander121

John long ago made the decision it would be his life for Rodney’s

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A Truth for a Truth by gottalovev

Severe solitary confinement is a bitch. Ask John.

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And Hope by Sihaya Black

While on a mission, John Sheppard discovers a device, but he doesn't expect what's inside.

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And this the life I gave for you by Lunabee34

Late at night while much of Atlantis sleeps, Rodney brings his laptop to the control room and works, one eye on the Gate. Watching for Sheppard.

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Ardhanarishvara by Auburn, monanotlisa

"Tell me, Colonel, did you take a look around and think, hey, it's the Planet of Sex Changes?"

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Awakenings by scherryzade

Rodney's the one who sleeps through the night, but not tonight...

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Baby Boom by darkmoore

"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?"

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Batman's Brain by savingfaith333

John’s gonna die saving the world someday, and Rodney doesn’t approve.

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Blink by lavvyan

I am going to tell you a story. About Dr. McKay and how he bought an eye from me, and how that one small act led to the strangest night in my entire life.

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Breaking the Mold by snowglow1275

This wasn’t like he’d simply been turned into a girl. That might be a little cool, for a while. But just knowing this body wasn’t his, that it had an original owner, one that would be getting it back, made him nervous about how he treated this body.

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Castles in the Air by silverraven11

Even after all these years, he's still a little in awe that he can have this. Prequel: Sandcastles but read this first.

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Catalyst by the_cephalopod

(Entry f'locked) Really, there is something seriously wrong when the highlight of their respective days is a game of chess. The mere idea that the attraction lies in something other than the challenge of the game is something on which Rodney steadfastly refuses to dwell.

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Clarity by Pollitt

"You needed me." It's probably one of the most honest statements John has ever said.

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Dawn Will Break by darkmoore, Cassandra Pierson (ca_pierson)

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.

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Day at the Beach by Soraya

This is the first story in a series, which deals with themes of death and loss. Sequels to this story are listed in the fic.

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Defract: Clear Blue Skies by senket

John Sheppard is obsessed with speed; it's only fair that he should have the shortest Ascension in all of history.

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Denial by ninefics

Rodney still has nightmares.

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Deprivation by mikes_grrl

Sheppard has a no-cross personal DMZ around him…until he doesn’t.

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Directional Theory by Rageprufrock (Glitterati)

Rodney does something stupid and pays with his heart.

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Dreams Are Never As They Seem by amy_thrace821

It's the twentieth time that John Sheppard has found himself in a cell, but it's the first time that his faith in his inevitable rescue has failed him.

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Epiphanies Aren't Just For Ancients (and Other Hard Learned Lessons) by djin7, reddwarfer

John Sheppard knows that sometimes, the quickest way to end a war is to lose it. But if he has to go down, he's taking Rodney with him.

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Finding Home by raicara

John is a Slave who ends up the property of one Dr Rodney Mckay

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Folie a Deux by Mad Maudlin

It matters like a hole in the head, because that's what it is: a hole, a wound, a fissure. He can feel out the raw edges where his memories have been cut to pieces, the sudden blanks where the film breaks and he is left flailing on the edge of words.

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Forever Home by kassrachel

John and Rodney find themselves far from home, with people that don't know the Stargate.

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Guilty Until Proven by Chensuu

Big Bang 2008. Forks in the Road: Outcast - John's brother Dave somehow becomes involved with the Replicators.

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Here Every Language Is Silent by enigmaticblues

Sometimes, you don't know what you have until it's gone.

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Home In Time For Jeopardy by shakespherical

Even the defeat of the Wraith and a bright future in the Pegasus galaxy doesn’t mean that the universe isn’t ultimately random and cruel. Or that love can’t be found in the ruins of your own life.

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Hugging the Fleece by SexyCazzy

John couldn't sleep while Rodney was in the infirmary.

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If I Could Start Again by hullfire

John is cheating on his wife with Rodney.

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In the Blood by Keira Marcos

"It really shouldn't be funny but you know I've always sort of suspected that we'd have a joint funeral."

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Integration by Parts by wneleh

Rodney breaks through Fortress Sheppard. With Math.

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Inukshuk by murron

Another mission-gone-south isolates Rodney and John from the rest of the team. Forced to search for an Ancient outpost, they struggle to keep each other alive until the time their kidnappers prepare to sacrifice the one and purify the other.

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It's a Small World After All by pir8fancier

FUBAR happens on Atlantis, John disappears, two years later Rodney takes a vacation to Disneyland, and who do you think is working at Soaring Over California?

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Judas Doesn't Answer by Auburn

O'Neill and Woolsey arrive in Atlantis along with SG-1. Shortly thereafter, Sheppard and McKay find themselves in a race to catch a murderer.

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Kill the lights and lock the door by less_star

No kisses, but no lies either, Rodney thinks. He keeps telling himself there won’t be a next time.

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Kiss Me Not by Lady Anne

Rodney waits for Sheppard’s return after Sheppard is taken by wraith worshippers

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Last Man Reshuffle by pir8fancier

"He earned those stars. If you put them down like the nice little impostor you are, I won’t shoot you. Maybe."

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Law of Martyrdom by pir8fancier

Post-season story. Rodney and Jennifer get engaged. The inevitable happens.

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Lifted by deltacephei

Something in John finally decides it's not worth waiting for any longer. Sequel: Alight

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Limiter by beachlass

In a way, it's easier once Rodney's dating Jennifer.

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Long Distance Call by fawkesielady-ed

For the Twilight Zone challenge - Rodney's dead so how can he answer John's phone call?

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Long Way Home by kimberlite

Returning to Earth stirs up hidden yearnings and ghosts from Sheppard's past.

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Lost Memory by annieb1955 (Annie Booker)

It’s cold when he wakes and he feels around for the covers, freezing as his hand encounters empty space next to him where Rodney should be.

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Message in a Bottle by mikes_grrl

John brought up the strangest things when they were having sex, but Rodney learned to just railroad past the weird and get to the good stuff.

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Might as Well Live by Rheanna

John was sure he was going to be re-assigned elsewhere...

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My Favorite Colonel by pir8fancier

AU based on the Cary Grant/Irene Dunne 1940s classic movie, "My Favorite Wife."

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No Good Deed by blackchaps

Rodney makes a plan and waiting is the hard part.

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No Longer All Right by reddwarfer

He can remember the times they used to stand side by side on the balconies, watching the weather, the sun, the rain, the clouds. Remix of And I say It's Alright

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No Refunds or Exchanges by shalott

Atlantis head scientist Rodney orders a mail-order bride. He gets ex-military pilot John instead.

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Nobody's Hero by sharkie335

"You stupid flyboy. Just have to risk your life at the slightest possibility. What is this, a deathwish? Are you out to kill yourself?"

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Nothing So Fragile by mckays_girl

Good intentions go awry and make things worse.

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Of the Spotless Mind by Lunabee34

Amnesia fic heavily inspired by The Eternal Sunshine of the Spotless Mind

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Once More With Feeling by soleta

he's a genius. that doesn't mean he can't be stupid every once in a while

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One Man's Island by lavvyan

John is a quarter werewolf.

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Out in the Open by xparrot

It's Situation Normal for the team when they're caught in an avalanche, but digging themselves out uncovers more than they counted on.

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Paradigm Shift by scherryzade

How did a sweet kid like Keller turn John into such a- Followed by: Three Weeks Later and Served Cold

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Piece by Piece by nakatas_cat

John gets interrogated mentally by telepaths and is forced to relive some very personal moments of his life in the Pegasus galaxy. Rodney doesn't leave his side and tries to come up with a plan to free John.

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Pilgrimage by trillingstar

Carson's mom was what Rodney had pictured, both sweet and sour, with wide, smiling eyes and prone to express fond exasperation, just like her son.

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Placebo by almostnever (Cesare)

"You might cut it off... Ronon has knives. You drilled into my head with a, a drill," Rodney said weakly.

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Planet Claire by saffronhouse

"It has to do with a rare verb form, the real-universe optative mood. It's used only for things happening in the real universe."

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Please Be Okay by psychicvanity

Twelve stupid hours, the gate would be offline. And all the while John Sheppard was coughing his lungs out thanks to some alien swamp virus.

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Pocket Full of Kryptonite by margarks

Big Bang 2008. Forks in the Road: Outcast - John goes back to Earth with Rodney instead of Ronon.

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Rainy Days by elizaria

When it's rainy and cold and he misses the halls of Atlantis and the way she'd turn up the heat for his morning shower; Rodney's POV: When the Rain Lets Up

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Rebound by rosiepaw

John learned then that the most important rebound rule of all is: never get involved in with someone on the rebound if there’s any chance you might fall in love with that person.

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Redux by Lunabee34

Just how many times has the Team had its memories wiped?

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Rescue by Zinnith

John closes his eyes and lays his head back down and thinks that it would be nice if someone came looking for him.

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Rescuing Rodney by Helenkacan (aka Helena K)

Rodney's not quite all there because of an accident with -- what else -- Ancient tech. John can't really do anything for him but wait. During the waiting comes the despair, writing and hoping.

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Rosemary, for Rememberance by Mhalachai

And then there was the time John Sheppard turned into a girl and no one thought it was strange but Rodney McKay.

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Sanguine (Blood on the Tide) by gothphyle

John thought he was used to the dangers of Pegasus, but he never anticipated this.

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Second Chance by sgamadison

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.

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Second Time Around by sgamadison

Not everyone gets a second chance... Sort of coda to Second Chance but can be read stand alone.

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Serendipity Lost by ribbon_purple

â€"Did you know the weather’s always the same here? Absolutely perfect all the time.”

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Sholdn't by lierdumoa

John and Rodney make up for lost time in a porny way.

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Shrapnel in his Skin by Claire

He can't go to Teyla with this. And there's a hundred reasons why it can't be Lorne.

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Sometimes a Spark Is All You Need by roaringmice

You think you'd know a man after 3.245 seconds.

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Still by murron

Remorse after a night of drunken sex and a mission in danger of going bad.

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Stockholm Serenade by busaikko

Neither of them is who they used to be.

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Strength by crystalheaven

Rodney's in the infirmary after a mission gone bad.

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Talking Points by pir8fancier

He managed to get out a raspy, "Congrats." It was the last word he spoke for months.

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The Air That Angels Breathe by Keira Marcos

Mutant!Verse. John has hid his mutation all of his life and then everything changes in an instant.

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The Bribe by Fenchurch

Rodney given to John as a slave and they're on their way to Atlantis.

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The Chair by Goddess47

Sitting in the Chair changes more things than John would have thought.

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The End of the World as We Know It by lavvyan

John Sheppard lived in a small house by the end of the world, which is just a few miles to the south of the left end of the rainbow. It was a solitary life, the house surrounded by nothing but long grass and wild flowers and a few trees in the distance... and, of course, the sheer cliff dropping straight down into infinity about fifteen feet from the back door.

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The Fourteenth of Green by kanata, kyuuketsukirui

It has been three weeks. Rodney marks another line on the wall. These ones are in red, a clean break to mark the days without John.

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The Fourth Part of the Night by siriaeve

But he knows that for six days, fifteen hours, nine minutes and an eternity of seconds, John is a couple of hundred yards and a solid wall of metal and marble away from them, from him.

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The Innocent's Dark Seduction by Goddess47

"Pregnant? Yes," Rodney snarled. "Now that Dave's devious plan has worked, you know about it. Yes, it's yours. No, you don't have to have anything to do with it... her......"

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The Kids Are Alright by nakedwesley

Big Bang 2008. Forks in the Road: Outcast - John goes back to Earth with Rodney in addition to Ronon.

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The Long Engagement by omg_wtf_yeah

McShep Steampunk!Atlantis AU. John is the leader of the Sheppard Circus Company. Lost in their travels, the troupe happens on the hidden city of Atlantis where McKay is the mistrustful leader of the Lanteans. McKay makes an agreement with the troupe wherein they'll stay on in the city and perform a number of shows. He also asks John for his adopted sister, Jennifer Keller's, hand in marriage. When John refuses to give them his blessing, Rodney proposes that the only way to change his mind is to get to know each other better. But as the two men become close, Rodney begins to question if marrying Jennifer is what he really wants or if what he wants could be something totally unexpected.

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The Sacrificial Mage by taste_is_sweet (Leah)

Magic was a zero-sum game. If you didn't sacrifice as much as you were given, you would lose.

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The Sorcerer King by Tarlan

In a time of magic, when Prince John mounts a rescue to save his family's oldest friend, he discovers more than just an ally in the sorcerer, Rodney McKay, as they seek to overthrow the Wraith Queen of Atlantis.

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The silence of the stars and of the sea by Anonymous

Rodney threatens to go back to Earth. John will do anything to make him stay, and Rodney's not above taking advantage.

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These Pages are Burning by deltacephei

This Wraith queen was different....

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Thousandmother by Springwoof

A run-in with the Wraith results in the Team being separated and stranded on a cold, harsh planet without help or supplies. As they struggle to survive and find each other, the Team discovers a new alien race and secrets that the Ancients left behind. Including a secret about Ascension that neither the Ancients nor the Ori want anyone to know.
AU sometime after Season 3's Common Ground.

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To Serve And Protect by Lenore

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.

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Transcendental by shalott

In less than a day, Rodney had blown past Elizabeth, Colonel Sumner, Colonel Markham, Colonel Escobar, and was rapidly coming up on Colonel Ryers as the absolute worst commanding officer John had ever had to report to.

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Tremblor by Chicklet

It's not that you haven't been held at gunpoint before.

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Trinity's Fall by lavvyan

Rodney thinks he's tried hard enough by now.

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Trope by solvent90 (solvent)

So there were these aliens, and they made them do it. And then there was obliviousness.

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True Peace by velocitygrass

Rodney waits and fears that the next letter will notify him of John's death.

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Until it's All You're Holding on Too by skitz_phenom

After tragedy strikes, Rodney's friends watch as he tries to do everything in his power to find a way to set things right. Sometimes the lengths Rodney McKay would go to on behalf of John Sheppard amazed even him; especially when those lengths included not being able to tell a single person about what he'd done.

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Waiting for My Real Life to Begin by toomuchplor

Rodney turns 40, dates Jennifer, kisses John and finds an Ancient weapons lab. Sequel: A Month Of

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Watch the Man by teh_gandu

McKay/Sheppard, unrequited McKay/Sheppard/Beckett.

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What the doctor would have ordered by shao_fu

Rodney takes Carson's death very hard.

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When you know you were born to fly by justbreathe80

John is a commercial pilot, Rodney is a difficult passenger.

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With These Wings, I- by senket

Rodney (is a sex god) simply can't afford to sleep with John Sheppard.

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Zombies and Blackouts -- Oh My by Catheights

Sometimes the Pegasus galaxy was the ultimate horror show, the fright never ended.

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he alone determines by thisissirius

Half-way through the celebration feast (there seemed to be one every three planets, now) a group of masked raiders had attacked the village.

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Stargate Atlantis Slash Index © fictionresource.com & the Stargate Atlantis Slash Index project team 2006-2009. All rights reserved.
Stargate Atlantis is © MGM Television Entertainment . No infringiment is intended.