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:
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 1, 2008
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.
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.
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.
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.
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.
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."
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.
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."
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.
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
Sentience, by Tarlan
John Sheppard/Rodney McKay, Jack O'Neill/Daniel Jackson. 62,200 words. An AU. What if Atlantis was sentient?
Slouching Towards Bethlehem, by Mrs Hamill
John Sheppard/Rodney McKay. 32,200 words. It was a day just like any other when it all went to hell.
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.
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.
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.
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.
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.
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.
*new*
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.
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, by Sapote3
Rodney McKay/Laura Cadman, Rodney McKay/John Sheppard. 14,500 words. In free Lantea, eight years after the war ends, all the children look like John Sheppard.
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 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.
While You Were Out, by Mad Maudlin
Gen, John Sheppard, Rodney McKay. 1,893 words. The last thing John remembered was exploding.
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.
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."
The Complexity of Daily Life, by Teaphile
Teyla Emmagan/Rodney McKay/Ronon Dex/John Sheppard. 34,830 words. We're the refugees this time, John. Elizabeth sat down, narrowing her eyes at him. Better get used to it.
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.
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.
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.
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
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.