When Jared/Sam is or interacts with aliens...as always, heed the warnings where the original story is posted. And please consider leaving a comment. It’s all the writer ever gets in return for their time, effort and generosity!
At the End of the World by ashtraythief on Ao3. Jared/Jensen. J2 AU. Jensen collects the wonders of the verse to preserve them; only observing, never getting involved. When he comes to a planet called Earth, he realizes he’s capable of deeper emotions than he was designed to have.
Grave series by all_the_damned_vampires on Ao3. Jared/Jensen. J2 AU. Â Jared is pretty sure he was insane even before he was abducted. Not many people can survive a global pandemic with their minds intact.
For a long time, it’s just Jared alone in the room, tended and manipulated by an unseen force. (past Jared/Adrienne in flashbacks)
Chasing Darkness by ashtraythief on Ao3. Jared/Jensen. J2 AU. Discharged from the military after the war and unable to find a regular job, Jensen and Dani end up on JD’s mining planet Wora. It’s one of the most hostile environments in the Old Galaxy, but the pay is astronomical. The job sounds easy enough: protect the miners. While battling the demons of his past, Jensen meets Jared, a beautiful, sought after companion, who is isolated by his own secrets. Jared had come to Wora, dragged by Chad, with the need to make some serious money. It doesn’t take Jensen long to figure out Jared’s secret and he has to decide how much he’s willing to risk to protect him.
As Boundless As the Sea by cherie_morte on LiveJournal. Jared/Jensen. J2 AU. Â Jensen is an Engelon, a race whose home planet was abandoned thousands of years ago. Now what remains of their collective live in a large spaceship that travels to find, conquer, and drain new planets and their inhabitants of the one precious substance they need to survive: water. Â When Jensen unintentionally takes a human form, his fellow Engelons have finally had enough. They cast him down to Earth, far from any ocean, where it is assumed he will die without access to water. But Jensen is rescued by Jared, a man who lives alone on the farm Jensen was dropped on. Jared has lost everything he ever held dear, but he has not lost his kindness or his willingness to help a very strange stranger in need.
Close Encounters by morganoconner on Ao3. Jared/Jensen. J2 AU. This is the story of how an alien named Jensen and a human named Jared met, fell in love, and got their happily ever after. (no penetrative sex)
Mission Voyager by soulmatecest on Ao3. Jared/Jensen. J2 AU. Earth has been colonized by a non-violent and pacifist race of aliens who have the ability to morph their bodies to look like humans and be able to live on this planet. But they believe real humans to be too violent and dangerous to keep around. It has been almost two years since Jared Padalecki ran to hide with a group of survivors, living in abandoned buildings and stealing supplies to survive.
I Can Fly (But I Want His Wings) by mystik on Ao3. Jared/Jensen. J2 AU. After a tragic death a couple years ago, the life of nineteen year-old Jared can be described in one word: numb. But one day, he meets a man that can change his life for good. A man that is literally different from anyone he ever met and that will turn not only his present, but his past upside down. Aliens are real after all. (warning: background Jared/Sandy (nothing explicit) and past Jared/Chad)
The Ethereal by saucyminx on Ao3. Jared/Jensen. J2 AU. Jared Padalecki had just about settled into his place as a member of the Earth Division squad aboard space station TwoTwo, ready to follow in the line of his family’s military linage. But everything he knew was about to change when an otherwise average day had him crossing paths with a should be extinct Ethereal. Especially when, against all odds, Jared found himself drawn to the half breed he’d been raised to despise.
World Domination is Harder than it Looks by kellifer_fic on LiveJournal. Jared/Jensen. J2 AU. Jensen Ackles is an alien and Jared is hell-bent on cuddling exposing him for what he is. (no penetrative sex)
The Third Kind by BewareTheIdes15 on Ao3. Jared/Jensen/Misha. J2/M AU. "So you see too?" Jensen whispers again, peeping around the edge of the bedroom door. The thing has climbed out from under the bedclothes and sprawled out in a long slice of sunlight pouring through the window. He's almost sure it wasn't that big last night. (no penetrative sex)
The Taking by morrezela on AO3. Jared/Jensen. J2 AU. Jared was on vacation on the mysterious and beautiful Parnath. He had known about the ‘takings’ that could happen; he just never thought that he would be that one tourist that would have it happen to him.
Legacy by c-is-for on LiveJournal. Jared/Jensen. J2 AU. Jared is a high school outcast, bullied for being gay and for having a father who had some strange theories before he disappeared. Jensen is a perpetual outsider, constantly on the move, trying to blend in as a normal teenager when he's anything but. When it comes time to make a stand against the forces pursuing Jensen, Jared discovers that his father's bizarre notions might have contained more truth than anyone realized. (only kissing)
The Squid Monster by morrezela on Ao3. Jared/Jensen. J2 AU. Jared picks up an intergalactic squid that decides to live on his inner thigh
Blood Feud by morrezela on Ao3. Jared/Jensen. J2 AU. Jared and his team were sent to evacuate a training facility on the latest colonized planet, but his mission wasn’t exactly successful. Now he either has to try to negotiate with the enemies who want him dead, or let a group of young cadets starve to death.
What About the Heart You Promised to the Tin Man? by misskittye on LiveJournal. Jared/Jensen. J2 AU. Jared Padalecki is a regular guy who runs into Jensen (literally) after watching a falling star crash into a lake. Jensen is more than meets the eye (while also being easy on the eyes) and he drags poor Jared into the plot of a sci-fi action movie. (no penetrative sex)
It’s Supernatural, Extraterrestrial by thorkiship18 on Ao3. Sam/Dean. Unrealated wincest AU. Dean Winchester is a Twenty-four year old truck driver with 0.3% of ties to the world around him. He's never had a long lasting relationship or a friendship for more than a week because he believes that everyone and everything around him is stupid.One rainy night, Dean almost runs down a young boy in the middle of the road. A boy who knows zero english and is ignorant to everything on Earth and also carries around a GPS like device that points east.Shenanigans and all types of fuckery ensue! (no explicit sex)
I Will Follow You by hunters_retreat on Ao3. Jared/Jensen. J2 AU. He did notice, as he’d turned, the way Jensen had licked his lips as he let his eyes trail over Jared one more time.  It may not mean anything.  It might mean everything.
Stardust and Hunting Go Hand in Hand by blackrose_17 on Ao3. Sam/Jack, Sam/Dean.  Sam Winchester was supposed to go to Stanford but a chance meeting with a Police Box changed his destiny and all those around him. Sam had known from a young age that Dean was his mate, his alpha but Dean didn’t see him as anything but a little brother. Jack on the other hand saw Sam for the omega he was and very interested. The last thing Dean ever expected to see back in his life was his little brother who’s heart he broke pregnant and mourning the loss of his lover. But together they realize that they are whole together and the other half of each other’s soul. (warning: mpreg)Â
Veterans of the Psychic War by kellwyntar on LiveJournal. Jared/Jensen. J2 AU. When the invasion came, no-one was ready. Humanity faltered. We died by the thousands, then by the millions. Nations fell before them before the survivors could begin to hold them back. At the most desperate moment in humanity's history, two men would face the battle. Jared Padalecki, a Psion whose power could only lead him to self-destruction alone in the face of the horrors of war, and Jensen Ackles, a Guardian fractured by his past. Apart, they are broken and incomplete. Together, they just might save the world, and maybe even themselves. (the sex is ambiguous)
Think of the Queen by kerfuffling on Ao3. Jared/Jensen. J2 AU. Â Jared never expected his ass to become the star of the show when he and Jensen find themselves trapped in a cave on an alien world.
Mayuon by hunters_retreat on Ao3. Jared/Jensen. J2 AU. Jared never believed anyone would be crazy enough to fund his research, but every crazier things had happened.  Like finding that his belief in an ancestor race was true and he'd found their home planet.  Or that the men he'd traveled with had turned out to be mercenaries, ready to kill the king and his people so that they could go back to Earth and start bringing people in to 'colonize' their new home.  Or that Jared could fall so completely in love with the king who hated him for the part he played in the mercenaries finding his people.  With a race against time, can Jared find a way to stop the ancient ceremony that would kill Jensen and his people?  Will he be able to stop the mercenaries in their plot to destroy the Martrikian people?  And will he find a way to show Jensen that he really is the man he believed he was when they fell in love?
The End (of Something) by ashtraythief on Ao3. Jared/Jensen. J2 AU. Jared and Jensen are captured by the enemy. In the face of almost certain death, Jensen finally makes a move. (no penetrative sex)
Garden of Ackles by morrezela on Ao3. Jared/Jensen. J2 AU. Long ago, Jensen Ackles was in an accident that left him in a wheelchair for life. He didn't let that stop him from amassing a small fortune and buying his own mansion at a dirt cheap price - no pun intended. But the mysterious gardens needed some work done, and Jensen couldn't do that with his own power. He hired Jared to be his gardener instead.
It’s Supernatural, Extraterrestrial by ghostboi on AO3. Jared/Jensen. J2 AU.  The far-reaching Love Story of Sam & Dean grabs the attention of some real big fans. (kissing only)
The Right Language by hunters_retreat on Ao3. Jared/Jensen. J2 AU. It would be lectures all day and it would only end when Jared was taken to the Crowned Prince for the ceremony.  Hopefully, a translator would be found before then.
Alien!Crack Verse by Annie46fic on Ao3. Jared/Jensen. J2 AU.  Jared and Jensen have the best ‘How we met’ story ever (warning: mpreg)
The Real World: New New York by DarceyDelaney on Ao3. Jared/Jensen. J2 AU.  Hundreds of years in the future, Jared takes part in Earth’s latest attempt at a reality TV phenomenon—they’ve revamped The Real World, but this time around, it’s taking place in space, specifically New New York, Mars. Jared originally signs on just to get Chad to shut up, but when he meets Jensen, his shy, really really ridiculously good-looking Martian housemate, he decides reality TV might not be so stupid after all. (the sex is ambiguous)
What Comes Next, Alien Sex? by zempasuchil on Ao3. Jared/Jensen. J2 AU. Jensen really IS too beautiful to be human. His true alien form is a little... strange. (chapter 2 is Jensen’s backstory where he does bottom for an OMC).
One for the Book by ashtraythief on Ao3. Jared/Jensen. J2 AU. Jared loved his job as ambassador to the Space Council. He especially loved to sample local customs.
Abductions and Amnesia by hunters_retreat on Ao3.  Jared/Jensen. J2 AU.  Jensen was a Prime and his dedication to Jared would never allow room for someone else. He would wait on Jared forever. Jared just wished it was love he saw in the other man’s eyes and not just the unswerving loyalty of a Prime that had been trained into him with his devotion. (the sex is ambiguous)
Forced Entry by virtualpersonal on Ao3. Sam/Dean. Wincest AU. Captain Winchester doesn’t like people messing around in his mind. He’s had some run-ins with telepaths and he hates them all. Too bad he's been paired up to work with Sam Wesson, one of the highest rated Telepaths in the Tel Unit.
My Favorite Martian by Ephermeralk on Ao3. Sam/Dean. Wincest AU.  When a space capsule crashes onto the beach where Dean’s working as an astronomer, he expects a NASA astronaut inside, not a humanoid extra-terrestrial named Sam. And he definitely doesn’t expect them to have much in common--like, say, being brothers. After all, his own brother Sam had died years ago in what was supposedly a house fire.
Deja Vu bu Zara_Zee on Ao3. Jared/Jensen. J2 AU. Dean Winchester has a pretty sweet life. He works in construction; he married his long-time girlfriend, Carmen, straight out of high school; and he’s almost paid off a basic apartment in the Middle District. He may never have left his home district, let alone his home planet, but he’s happy… more-or-less.So why does he keep dreaming about the red wastelands of Mars? Why does he know more about the Martian Resistance than he has any right to? And who do the long, long legs and decidedly male butt that have him waking up achingly hard every morning belong to?Maybe Dean just needs a holiday? He couldn’t afford a real one, of course, but maybe he could go to Déjà Vu and get the memories of a holiday implanted; get Mars out of his system.Of course, that’s when the trouble really starts.
And I’m going to sneak a gen series in here. You can always read it with wincest goggles on.
Xenophobia by selecasharp and pixymisa on LiveJournal. Sam& Dean. Gen AU. In space, no one can hear you scream. And its sequel, Xenocide. This time, it’s war.