SGA thematic list: Atlantis is cut off from Earth or secedes

This is a SGA thematic list (i.e. not recs) for stories in which Atlantis is cut off from Earth or secedes, so that the expedition, either by necessity or by choice, has to fend for itself in the Pegasus galaxy. For a story to be included in the list the Atlantis expedition has to loose contact with Earth permanently, or at least for a significantly longer time than in canon, declare independence from Earth, or be stranded as a colony in Pegasus after Atlantis is lost. I've divided the list in the following subsections:

  1. Atlantis is involuntarily cut off from Earth, e.g. it's on its own because Earth has been lost or is too occupied in the Milky Way (overrun by Ori, Replicators or Goa'uld, blown up, hit by a natural disaster...), or has never (or only much later) reestablished contact in the first place; contact with Earth may or may not happen eventually, but the separation has had a lasting impact, and is somewhat central to the story.
  2. Atlantis intentionally secedes from Earth, i.e. declares its independence, or its allegiance to one or more Pegasus cultures/alliances or develops into a colony city in the (far) future.
  3. The Atlantis expedition members (i.e. more than just the team) settle as a colony somewhere else in Pegasus, e.g. because Atlantis the city has been lost to some enemy or disaster, or taken over by Earth officials the original expedition can't support in their goals leading to mass desertion, or similar scenarios.

These are not recs, but a thematic list. I'll link gen stories as well as all kinds of pairings, but at least initially it's biased towards pairings I read, e.g. I don't read John/Elizabeth so I'll need others to point out stories from those corners of fandom fitting the list criteria to me.

If you want a story added, your own or others, please send me the title, author, pairings (if any), summary, a public link (i.e. no f-locked or community member locked LJ entries and the like), whether it's a WIP, and under which topic it'll fit, so that I can list the story.

Last updated: November 19, 2014

1. Atlantis is involuntarily cut off from Earth.

After the Fall, by Settiai
Rodney McKay/Teyla Emmagan. 1,300 words. Three months later, everyone's hope was dwindling.

All the Things Rodney Never Was, by Sardonicsmiley
Rodney McKay/John Sheppard, Lorne/Parrish. 8,270 words. Rodney wasn't trained for this.

And All We Have, by Seekergeek
Rodney McKay/John Sheppard. 49,000 words. Earth is gone, lost to the Ori and Atlantis has to take a hard look at how to survive now that they're on their own.

Asylum, by Jenwryn
John Sheppard/Rodney McKay, Evan Lorne/Teyla Emmagan. 390 words. AU, in which our people are refugee-settlers in the Pegasus Galaxy.

Blue, by Sorrel
Rodney McKay/John Sheppard, Rodney McKay/Ronon Dex, Rodney McKay/John Sheppard/Ronon Dex. WIP. AU from Conversion, where John's mind is saved from the retrovirus but his body stays the same. Not long after that they lose contact with Earth and have to fend for themselves.

Center of the Sun, by Auburn
Gen. 5,255 words. Excerpt from a longer, incomplete work. Conceived in 2007 and written intermittently over 2008 and not canonical. Posted for Fictional Amnesty Day.

Charming Demeter's Daughter, by wolfshark
Rodney McKay/John Sheppard, Teyla Emmagan/Kanaan. 43,404 words. 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?

Dancing Stones, by Auburn
Gen. 4,375 words. Excerpt from a longer, incomplete work. Conceived in 2007 and written intermittently over 2008 and not canonical.

*new* Decade by canis_lupus
John Sheppard/Rodney McKay. 63,104 words. Ten years ago, an expedition left for Atlantis. They were never heard from again.

The Directory, by Tarlan
Rodney McKay/John Sheppard. 1,481 words. Being separated from Earth meant making sacrifices, and pooling resources.

Draconian Measures, by Tarlan
John Sheppard/Rodney McKay. 54,851 words. Following on from the Stargate SG-1 episode, 'The Road Not Taken'. Rodney is coerced into taking over Sam's role as President Landry's chief science adviser, but without another ZPM, he knows it is only a matter of time before the Ori return and destroy the Earth. However, the threat comes from an unexpected direction, and as Earth falls to the Goa'uld System Lords, who want to make Earth their final battleground against the Ori, Rodney and John organize the escape of those they are able to save using the last of Earth's ships (Daedalus and Prometheus) and the Stargate. As they battle to raise Atlantis and then power her, John and Rodney discover that the Goa'uld and the Ori are not the only enemy they must overcome before Atlantis can become a true refuge - and home.

Drawn To A Different Light by reyclou
Gen. 34,160 words. Team Sheppard finds an alternative Atlantis in desperate times, but soon learns appearances are not always as they seem.

The Dreaming, by Kat Reitz and Tzigane
Rodney McKay/John Sheppard. 13,080 words. When the Sickness came, they'd called it a great many things. At first, there had been laughter, joking references to Captain Tripps and the superflu, and then there'd been not so joking references to that and worse.

East or West, by Kat Reitz and Perryvic
Rodney McKay/Acastus Kolya, Rodney McKay/Carson Beckett, Rodney McKay/John Sheppard. 179,160 words. Left or right, east or west. He was remembering the direction of the stars. Remembering how he had figured the direction to Kandahar and Kabul from the sky. He knew how to navigate using the sky. The ground he found a little more tricky.

Eleven Moments, by Dianann
Samantha Carter/Jack O'Neill, Jack O'Neill/Daniel Jackson, Samantha Carter/Rodney McKay, John Sheppard/Rodney McKay. 5,700 words. The moments of Sam Carter's life, both on Earth and on Atlantis.

Ersatz Void, by Nixa Jane
Rodney McKay/John Sheppard. 16,315 words. The expedition left for Atlantis without Rodney McKay, but two years later, he catches up to them.

Give Me Your Hands, If We Be Friends, by squidgiepdx
Parrish/Evan Lorne, Elizabeth Weir/Radek Zelenka, Rodney McKay/John Sheppard (mention), Carson Beckett/Laura Cadman (mention). 2,015 words. No summary provided by the author.

Here In This Lonely Place, by Brighid
Rodney McKay/John Sheppard. 4,562 words. Rodney has always been stupid in love with John.

The History of Atlantis, Part II: The City as Recording Angel, by Mirabile Dictu.
Rodney McKay/John Sheppard, Laura Cadman/Carson Beckett, Lorne/Zelenka/Weir/Dex. A collection of stories set in an Atlantis that has lost contact with Earth, including with the Daedalus.

I Am Your Image Dressed as the World, by Mirabile Dictu
John Sheppard/Rodney McKay. 11,500 words. "I missed you so much," John whispered. "I didn't know. It was always me leaving, so I didn't know."

If All Else Fails series, by enigmaticblue
Rodney McKay/John Sheppard, Evan Lorne/OMC, Daniel Jackson/Vala Mal Doran, Sam Carter/Jack O'Neill. 149,736 words so far. Technically, it's known as Operation Phoenix, but that's a little too optimistic for Jack, who calls it the WAFGON plan: We're All Fucked; Get Out Now.

In This Era of Liberty, by Chandri
John Sheppard/Rodney McKay. 35,600 words. People are not like mathematics. They don't make nearly as much sense.

A Lament For the Living, by WritinginCT
Daniel Jackson/Ronon Dex. 4,944 words. Earth is destroyed and a lone ship full of survivors makes it to Atlantis. A guilt-ridden and emotionally spent Daniel is able to find comfort and healing in someone that knows the pain of his loss intimately.

Left to Fend, by Springwoof
Gen. 6,800 words. What would Elizabeth Weir do if she was abandoned? Anything she had to...
and its sequel/remix
The Body Holographic, by Leah and Springwoof
Rodney McKay/John Sheppard. 68,100 words. "I would give anything for you to be real."

Life After, by Velocitygrass
John Sheppard/Rodney McKay. 48,206 words. "We could do more," John said, turning to him, and there was a conviction in his voice and eyes that sent shivers down Rodney's spine. "We could destroy the Wraith."

New Lantean Chronicles: Lost City Found and its prequel New Lantean Chronicles: The First Year, by Chiara Crawford
John Sheppard/Elizabeth Weir, Jack O'Neill/Sam Carter, Peter Grodin/OFC, Keras/OFC. 101,320 words and 11,343 words. After five years of having no contact with Earth, the Earth-born New Lanteans are reunited with the Tau'ri. But five years in a different galaxy changes people, sometimes irrevocably.

On Their Own, by Wolfshark
John Sheppard/Rodney McKay. 17,843 words. What if the satellite worked? What if Earth hadn't come to Atlantis's rescue?

Peanut Butter and Chocolate, by Master Elayna
John Sheppard/Rodney McKay. 15,585 words. On an Atlantis separated from Earth, Rodney finds a way to start a family of his own.

Qui Habitat, by Domenika Marzione
Gen, John Sheppard, Cameron Mitchell. WIP (the universe, individual stories are finished, ca. 143,000 words so far). AU that spins off from the Ori arc that runs through Seasons Nine and Ten of SG-1 by changing one simple thing: the Ori don't lose. Earth is the last significant planet to fall in the Milky Way, but fall it does. Hard.

Retrograde Series, by Martha Wilson
Gen. The Atlantis expedition has been lost for three years. SG-1 goes to find them, and arrives just a little too late.

Riches, by Luthien
John Sheppard/Rodney McKay. 100 words. Cut off from Earth for good...

Season For All Things, by kat_lair
Gen, team. 2,500 words. To every thing there is a season, and a time to every purpose under the heaven ~ Ecclesiastes 3:1

Second Siege, by americanleaguer
John Sheppard/Rodney McKay. 7,626 words. The Second Siege is not a battle.

Sentience, by Tarlan
John Sheppard/Rodney McKay, Jack O'Neill/Daniel Jackson. 75,079 words. An AU. What if Atlantis was sentient?

Slouching Towards Bethlehem and its sequel And There Was War in Heaven, by Mrs Hamill
John Sheppard/Rodney McKay. 32,200 words and 50,200 words. It was a day just like any other when it all went to hell.

*new* Some Corner of a Foreign Field by neela
John Sheppard/Samantha Carter. 224,699 words. With a Wraith superhive about to attack Atlantis, Colonel Samantha Carter had hoped for reinforcements from Earth. Instead she got refugees from an abandoned SGC and the message that Earth is lost. Apoca!fic. AU post-EatG.

Square Peg, Round Hole, by Wolfshark
John Sheppard/Rodney McKay. 56,170 words. When the Ori overrun Earth, some of the SGC evacuate to Atlantis, where they're just not fitting in. This causes serious issues.

Together They Have Built A World and A Lot Of It Is Real, by Sheila
John Sheppard/Rodney McKay. 41,254 words. "I'll never get tired of watching it land," John says, watching the Daedalus glide smoothly toward the city. Thirty seconds later it blows up.

Twilight of the Fifth Sun, by Tzzzz
John Sheppard/Rodney McKay. WIP. The world ends and a young John and Rodney are among the group evacuated to Atlantis.

Two Years After Tomorrow, by Lavvyan
John Sheppard/Rodney McKay. 1,500 words. Aneen didn't like Colonel Sheppard much.

Up Into The Silence, by Auburn
John Sheppard/Rodney McKay. 7,747 words. What happens if, when we open the Stargate to Earth, the only answer is silence?
and its mirror
Rosebud, by Auburn
John Sheppard/Rodney McKay. 3,517 words. He dreams of walking her hollow halls, but he cannot find his way back.

Upward Over the Mountain, by Auburn
Gen. 36,275 words. The first part of a longer, incomplete work meant as a gift for mirabile_dictu. Abandoned due to plot, structure and character faults that are inherent to the original concept. Conceived in 2007 and written intermittently over 2008 and not canonical. Posted for Fictional Amnesty Day.

Variations In D Major, by sian1359
Rodney McKay/John Sheppard. 73,618 words. Whatever happened to the original Atlantis expedition?

Vive ut Vivas, by Cassiejamie
Rodney McKay/Carson Beckett, Elizabeth Weir/Radek Zelenka, Ronon Dex/Teyla Emmagan. WIP. The grieving that follows a loss is real, and can be very painful.

Where the White Lilies Grow, by Eildon Rhymer
Gen. 44,400 words. People tell stories about the wonders of the Time Before. They tell stories, too, about magical creatures with long, fair hair, who emerge from the hill and can turn you to dust in an instant. But John Sheppard has never been one to believe in stories...

Your Inevitable Unhappy Ending, by Helen
John Sheppard/Rodney McKay. 14,300 words. It was easy to imagine fucking Rodney, the way he'd groan and clutch at John's arms and be too bossy about the whole thing; it was easy to imagine the problems it could cause.

2. Atlantis intentionally secedes from Earth.

As the Stars Fall, by flitterflutterfly
Rodney McKay/John Sheppard, Daniel Jackson/Jack O'Neil. 23,640 words .The expedition to Atlantis fails and is recalled back to Earth just in time to discover the ramifications of their curiosity. Mutations start cropping up all over the world, beginning first as a mysterious sickness. The SGC soon learns there is more to Ascension then they’d first thought as a new species of human is quite suddenly created.

Before & After, by helena_eternal
Rodney McKay/John Sheppard. 3,610 words. Governments will push and push, but there are times when The People push back. Zelenka's POV.

The Bridges Universe, by Miriel
John Sheppard/Rodney McKay, Elizabeth Weir/Ladon Radim. 28,000+ words. This universe spins off from canon as of "The Return Part 2" (03x11), and heads straight on 'til morning. It looks at an Alliance of desperation, an Atlantis that is independent out of necessity rather than choice, and both the people who live there and those left behind on Earth.

A Brief History of Time, by ZedElla
John Sheppard/Rodney McKay, Sam Carter/Jack O'Neill. 2,494 words. Here's the thing about Atlantis: it isn't Earth.

Colony Atlantis Series, by Enola Jones
Gen. Woolsey realises just where his loyalties lie.

Colony Atlantis, by Icarus
Jack O'Neill/Daniel Jackson. 7,300 words. This is what happens when Weir begins to build her vision of a utopia.

Colony!Atlantis Series, by Ismenetruth
Rodney McKay/John Sheppard. So in the fifth year of the expedition, which isn't even technically an expedition anymore since Elizabeth wrote a Declaration of Independence, which Sheppard will never, ever stop finding absolutely hilarious, Sheppard's still following the guidelines.

Crimes Against Humanity, by Jenn
John Sheppard/Rodney McKay. WIP. Atlantis was a neutral colony before it became a prison camp. Even Alcatraz is escapable.

Crossing Twilight, by Mystic
John Sheppard/Rodney McKay. 68,966 words. Events send McKay truly adrift, as he is faced taking on the universe to save the man he loved from the people ears trying to protect: Earth.

The Devil You Know series, by Telesilla
Rodney McKay/John Sheppard, Jeannie McKay/Ronon, Elizabeth Weir/Radek Zelenka, Teyla Emmagan/Kanaan. 111,148 words. 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.

Finding Home, by Diamond-Raven
John Sheppard/Rodney McKay. 54,960 words. When John continued staring at him blankly, Rodney thought he'd clarify. "We're going to run, John. We've got two weeks before the Daedalus gets here. Which means in a week and a half, we have to be long gone from the city."

Fugue State, by Miera
Gen, John Sheppard, Elizabeth Weir. 1,680 words. AU. Elizabeth's second encounter with the Pegasus Replicators has her declared a security risk, and the SGC is stonewalling Atlantis on her status.

Gather Us Poseidon's Children, by Liondragon
WIP. The lights were off in Atlantis when John woke up. That was the first thing that clued him in that something was wrong.

Götterdämmerung, by Mira
John Sheppard/Rodney McKay. 2,903 words. John felt Radek's hand on his shoulder. "Will you hinder us?" Radek asked him, earnest and somber.

I Have Loved the Stars Too Fondly to Be Frightened of the Night, by Mirabile Dictu
Rodney McKay/John Sheppard. 12,125 words. He did like that all the cadets were required to address him as "sir," though.

Into the Whirlwind, by Slybrarian
John Sheppard/Evan Lorne. 66,500 words. In his trip to the future, John saw a possible reality in which his team died and Earth abandoned Atlantis. He managed to prevent the first, but now the IOA has recalled Colonel Carter and replaced her with Richard Woolsey, as holo-Rodney predicted. Determined to insure a better future for Atlantis and the Pegasus Galaxy, he gathers a group of trusted friends to help him guarantee Atlantis will remain operational no matter what anyone else has to say about it.

Lantean Legacy - Book One: No Enemy Within, by Keira Marcos
Rodney McKay/John Sheppard, Radek Zelenka/Miko Kusanagi, Daniel Jackson/Vala Mal Doran, Evan Lorne/OMC. 66,900 words. 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.

The Memoirs Universe, by Miriel
John Sheppard/Rodney McKay, Lorne/Novak, Lorne/Parrish. 40,000+ words. An alternate future in which the ATA gene is a curse as much as a blessing, and Earth only ever looks out for itself.

No Light and Transient Cause, by Sheafrotherdon
John Sheppard/Rodney McKay. 21,500 words. Rodney McKay has an opinion on everything, including whether, in times of crisis, John Sheppard has any business risking death. Answer: no, don't be utterly stupid, what kind of ridiculous half-wit are you anyway?

Panthalassa and its sequel Pangeneses, by Sapote3
Rodney McKay/Laura Cadman, Rodney McKay/John Sheppard. 14,500 words and 16,000 words. In free Lantea, eight years after the war ends, all the children look like John Sheppard.

Pay No Worship to the Garish Sun, by rysler
Rodney McKay/John Sheppard. 1,400 words. Atlantis has seceded. Things go bump in the night.

Poems, Prayers & Promises, by Cyanne
John Sheppard/Rodney McKay. 10,000 words. An accidental proposal followed by a surprise wedding. It said volumes about his life. Their lives. And there wasn't a thing in the universe he'd trade it for.

Repercussions, by Crazy-obsessed
Rodney McKay/John Sheppard. 13,500 words. John is held hostage by Kolya and Elizabeth refuses to rescue him.

Shimmer, by Panisdead
Rodney McKay/John Sheppard. 800 words. The first night the fall temperatures on Atlantis dipped down below freezing, John had spent the entire day on the mainland digging post holes with Teyla, Ronon, and a squad of burly, ego-driven Marines, so when the wind from the open bedroom window chilled his ears and bare shoulders and set his stiffening back muscles to aching, he could barely rouse himself enough to whimper and burrow deeper under the covers.
and its remix
Always Summer, by Jenn
Rodney McKay/John Sheppard. 2,400 words. It flows like water over Rodney's hands, slipping between his fingers in shimmering green and ocean blue by turn, quilted layers as soft as down. It's warm, reminding him of cashmere and silk, of a distant planet he hasn't called home in more years than he can count.

The Slow Slide of Indifference, by Ladyholder
John Sheppard/Rodney McKay. 57,900 words. It had started out as a slow form of indifference. Slow like all the worst sorts of cancer were slow. You never really saw it until it was too late, but after words, the warning signs were all too clear.

The Surly Bonds of Earth, by Mad Maudlin
Rodney McKay/Jennifer Keller, Teyla Emmagan/Kanaan. 5,084 words. It turns out you can go home again.

10 Years and 1 Day series, by sarcastic_fi
Rodney McKay/John Sheppard, Elizabeth Weir/OMC, Teyla Emmagen/Kanaan, Vala/Daniel Jackson. 16,286 words. Au - in which the people on the Atlantis mission agree to cut all ties with those on Earth until they can defeat the Wraith. When they finally reconnect with Earth, it has consequences they didn't expect.

The Water Grinds the Stone, by Auburn
John Sheppard/Rodney McKay. 242,740 words. When the Stargate Program goes public, old loyalties are set against new ambitions for the Atlantis team, but a deal with the devil to save McKay's life will bring everything full circle and leave Sheppard in need of saving too, when Earth finds itself in contention with the people of the Pegasus Galaxy.

When in the Course of Human Events, by hoktauri
John Sheppard/Rodney McKay. 1,142 words. After years of war, politicking and bureaucratic struggle, Atlantis declares independence from Earth.

Where to Start Over and How to Begin, by Lilyfarfalla
John Sheppard/Rodney McKay, background McKay/Keller, Teyla/Kanaan. 15,200 words. Post-Season 5, Atlantis is stuck on Earth. Teyla realizes she has to create the path to take Atlantis home. With the help of Woolsey, Ronon, John and Rodney, she's wildly successful, but somewhere along the way, Rodney and John get a little lost.

While You Were Out, by Mad Maudlin
Gen, John Sheppard, Rodney McKay. 1,893 words. The last thing John remembered was exploding.

Write Her Name in the Sky, by ladysorka
Gen. 2,332 words. Meredith was going to have a lot of explaining to do.

Written By The Victors, by Cesperanza
Rodney McKay/John Sheppard, John Sheppard/Teyla Emmagan. 53,500 words. Caroll, Franklin R. Atlantis Revisited. New York and London, Routledge, 2011. Chapman, Denise. Several Kinds of Genius: The Life of Rodney McKay. NY: Harper Perennial, 2015. Croft, Rosalind. City of Spires: A Memoir. Toronto: The Mercury Press, 2009. Dugan, Paul. A Political History of Atlantis. Oxford: OUP, 2012.

3. The Atlantis expedition members settle as a colony somewhere else in Pegasus.

Atlantis Wasn't Built in a Day, by Eleveninches
Rodney McKay/John Sheppard. 3,600 words. "It was just his luck to get stranded in a galaxy where he had to live in a wigwam and eat polar bear."

Cache Ta Vie, by Mirabile Dictu
Gen. 1,300 words. In honor of a sad Memorial Day, Cache Ta Vie, which is French for "hide your life."

The Complexity of Daily Life, by Teaphile
Teyla Emmagan/Rodney McKay/Ronon Dex/John Sheppard. 33,835 words. We're the refugees this time, John. Elizabeth sat down, narrowing her eyes at him. Better get used to it.

Damned If You Do, and Damned If You Don't, by pir8fancier
Rodney McKay/Jennifer Keller, Rodney McKay/John Sheppard. 23,268 words. They are now on Earth. People are making choices. Bad choices.

Down this Chain of Days, by Telesilla
Rodney McKay/Teyla Emmagan. 2,200 words. In which Rodney and Teyla work together, play together and Rodney does some problem solving that has nothing to do with physics.

East of The Sun, West of The Moon, by Dossier
Gen. 150,000 words. That which does not kill us, makes us stronger--Friedrich Nietzsche.

Endings Unexpectedly Happy, by Mirabile Dictu
John Sheppard/Ronon Dex/Rodney McKay/Teyla Emmagen. 6,000 words. In John's dreams, he saw again he and his team fleeing in a stolen puddle jumper; he saw smoke and steam rising from Atlantis as they circled away, heading to the nearest orbital stargate and into the black of the Pegasus Galaxy, so thick with worlds yet so thin with stars.

*new* Eudaimonia by miera
John Sheppard/Elizabeth Weir, Carson Beckett/Teyla Emmagan. 18,630 words. They were cut off from Earth (again) and on their own for everything, beginning with bare survival. The hope of getting Atlantis back was slim. John wasn't going to give up, and he knew Elizabeth wouldn't either, but in the short-term, they had to focus on more important matters.

Hail Mary, by Kat Reitz and Perryvic
Rodney McKay/John Sheppard. 13,450 words. He said he didn't want to talk about it. About her, his Thera and so... they didn't.

(Im)possible Universes, by Wojelah
Gen, team. 2,150 words. McKay likes to talk about alternate universes a lot. Actually, McKay just likes to talk.

An Inland Soul to the Sea, by Mirabile Dictu
John Sheppard/Rodney McKay. 3,900 words. Written for the Casa McShep Summer Fiesta.

Into the West, by Leanne
Gen, Elizabeth Weir. WIP, 2,939 words so far. No summary by the author.

Ishmael, by Lavvyan
John Sheppard/Rodney McKay. 2,264 words. Rodney has never viewed himself as a particularly self-sacrificing person, but standing in his burning city, watching the last jumper headed for the mainland take off into the night sky, he finds that what he feels is more relief than fear.

A Knot Better Left Untied, by reddwarfer
John Sheppard/Rodney McKay. 5,200 words. Rodney finally finds a ZPM.

The Matchmaker, by Lavvyan
John Sheppard/Rodney McKay. 4,228 words. Nelan goes to see the Matchmaker.

Not Dead Yet , by Exploded Pen
Gen, team. 757 words. It's been almost a year, John thinks, as he watches over the others at night. Almost a year since his team tried to dial Atlantis and failed. One hell of an anniversary to have.

nothing else but the mysterious pull of the moon, by Mirabile Dictu
John Sheppard/Rodney McKay, Teyla Emmagan/Ronon Dex, Elizabeth Weir/Radek Zelenka, Lorne/OFC. 21,140 words. They really were evacuating Atlantis.

Pick Yourself Up, Dust Yourself Down, by Blinkiesays
Rodney McKay/John Sheppard. 3,640 words. John only has a moment to boggle at the fact that Elizabeth knows what a Tyrolese Grey is and what it looks like before he boggles harder at the fact that they've ended up in an uninhabited parallel Stargate-less universe with cows.

The Origin of All Things, by chocolatephysicist
John Sheppard/Rodney McKay, multiple other pairings. 115,400+ words, WIP. Something goes wrong during the evacuation of Atlantis, stranding members of the Atlantis expedition and SG1 on a very strange world.

*new* Pegasus Galaxy's Lost and Found Section by Stella Wind
Aiden Ford/Rodney McKay & Teyla Emmagan/Sora. 15,278 words. When the Ancients return to Atlantis, Rodney chooses not to return to Earth. He finds there are still so many lost things to discover in the Pegasus Galaxy.

Something Like Home, by Mirabile Dictu
Rodney McKay/John Sheppard/Ronon Dex/Teyla Emmagan. 11,000 words. And a man shall be as an hiding place from the wind, and a covert from the tempest; as rivers of water in a dry place, as the shadow of a great rock in a weary land. -- Isaiah 32:2

Speaker for the Dead and its sequel Jeden Dobrý Člověk, by MrsHamill
John Sheppard/Rodney McKay, Ronon Dex/OFC, Radek Zelenka/OFC. 10,800 words and 5,540 words. Only solitary men know the full joys of friendship. Others have their family; but to a solitary and an exile, his friends are everything. (Willa Cather)

Survivors War, by marysuewriter
Rodney McKay/John Sheppard. 3,452 words. What if SG1 hadn't gotten the ZPM? The last survivors of the Atlantis Mission struggle to live in hiding in the Pegasus galaxy.

That Will Break You, by mz_bstone.
Rodney McKay/John Sheppard, Rodney McKay/Jennifer Keller. 8,500 words. Life can break your bones. It can also stitch you back together.

This Tardiest Explorer, by Mirabile Dictu
Rodney McKay/Teyla Emmagan, Rodney McKay/John Sheppard. 8,341 words. All good love stories begin with a kiss.

Triptych, by Mad Maudlin
Gen. 4,800 words. They actually created this universe the moment they activated the time-travel device, and so their actions in the past were always part of our timeline. If they had tried to return to this present, they'd have run into their own doubles who never traveled back, and, well, that would be terribly awkward, wouldn't it?"

Who's Left and Who's Leaving, by the_drifter
Gen. 9,500 words. "No names," Rodney tells them, one more time. "And no dates -- I'm serious about that. No one can know what anyone else is planning." John learns the structures of life and death.

*new* Your eyes turned skywards by neela by neela
John Sheppard/Samantha Carter. 8,758 words. The plan had failed. John didn't know how, but somehow it'd failed. Instead of taking the Asurans with their pants down, the Replicator humanoids had stood ready. ... It'd been a massacre.