Sam and Dean are still brothers. They were placed in the foster system after John Winchester was tried and (wrongfully) convicted for the murder of his wife, the arson that covered it up, and endangering his two children. To protect their identities, they were listed as Sam and Dean Wesson in the system.
Little Dean took it as his purpose to take care of Sammy, because that’s the last thing his daddy said to him before they took him away. However, Sam being tiny and cute and the baby everyone wants, was quickly adopted by the Moores, who thought that they couldn’t get pregnant. (A year-and-a-half later, Jessica came along, which neatly explains why Wesson’s fiancé is Madison, not Jess.) Unfortunately, Dean, while also young and SUPER cute as well, had some emotional and behavioral issues (such as refusing to speak since the fire), which made him less desirable as an adoptee. Since the Moores were deemed unable to support a second child, especially one who would need special care, Dean and Sam were separated.
This backfired in a weird way, in that five/six-year-old Dean basically lost the last sense of himself he’d had and began to repress his past experiences, becoming essentially a blank slate that would adapt to whatever he thought a potential family might like. When he was finally adopted by Robert and Ellen “Smith”, his mind replaced Sam with Jo, and he came to believe that they were his original family.
(Bill had been killed much earlier in this timeline, in an incident that took out the Roadhouse. Bobby took Ellen and baby Jo in and eventually the two started a romance. After a dangerous supernatural episode targeting Singer Salvage nearly kills them all, Bobby and Ellen decided to get ‘out’ and try to make a new life. They called in quite a few favors to get their new identities and affairs in order. You wouldn’t think a couple like that could adopt a child so early, but Missouri [who unsuccessfully testified in defense of John, and had fostered Dean for a while] guided them through it.)
Dean’s mental block about his past kept the Smiths from telling him, out of a fear of relapse. Jo doesn’t know either (she even know about her father). For one, they believe family doesn’t end with blood, and two, they thought it would be safer if the kids believed what they wanted. (Just think of it kind of corresponding to Bobby not saying anything about Sam being alive, but over an extended period of time.)
So Dean Smith grows up without the hyper-masculinized hunting lifestyle, hence his much looser presentation compared to Dean Winchester. He’s more uptight in other areas, retaining that patented Dean self-loathing, which manifests in body dismorphic disorder and possibly a minor variation of OCD. There’s this weird void in him, which leads to an over-achiever type attitude and a desire for normative “success” to make up for what he perceives as lacking in himself. He retains that adaptability he formed in his childhood which makes him a great salesman/advertiser. (For instance, I see Smith as higher on the Kinsey scale than Winchester - or at least more aware of it - but that perceived “lack” of normality [perhaps knowing he might never give his parents grandkids, or thinking that he’ll never find someone who would want him and want to STAY with him] drives him to compensate by being a good businessman and bringing in good money to support his family back home and his sister in school. Even if he really wanted to stay close and be a fireman, a SPCA cop, mad inventor, or whatever.)
Even though they had Jess, the Moores still loved and raised Sam as their own. Sam figured out at a young age to he was adopted. However, they never told him he had a brother, thinking there might be trouble. Without John and the supernatural to struggle with, Sam Wesson (he took what he thought was his original name when he left home) has fewer anger issues as well as exposure to fewer acts of injustice. Instead he applied his mad research skills [and reliable access to an internet connection in his teens] to information sciences. He did not anticipate the cubicle, but hey, weddings and college loans are expensive and it’s a job. Sam Wesson still has prophetic dreams, although they started earlier and were not often death omens. Some, as we’ve seen, are a possible link to alternate realities. Others dealt with Dean, half a continent away and missing something he couldn’t remember.
Things happened mostly like they did in the episode, excepting of course, that it wasn’t an angelic lesson (or if it was, it was a primer to ease them in to the concept of the supernatural before throwing them headfirst into the apocalypse, in which case Mr. Adler just smiles his shark’s smile and gives Dean Smith and Sam Wesson both unprecedented departure bonuses, leading some to whisper about corporate espionage and/or blackmail money because that man is frankly creepy). It also happened a little bit earlier in their lives than the actual episode was. Probably somewhere early/mid Season three (about a year earlier). The two men do set off to save people and hunt things, not without a few pitfalls. Dean insists on healthy eating and on never flying again if he doesn’t have to. Money is a little tight, even with the money Sam no longer has to pay for the wedding and the extensive bonuses they had mysteriously earned. But hey, Dean has a Prius, so they get pretty good fuel economy.
Their second hunt (after Sandover) started out as Sam checking on Madison. Unfortunately, they were too late for her and another hunter was already on the werewolf case. Roy and Walt? (Not Gordon, because Gordon is NOT the guy you want training you in the lifestyle, especially if you’re two relatively happy do-gooders who haven’t had anything bad happen to them [that they know of].) She still asks Sam to kill her, and he does.
They stick with Roy and Walt for a bit, then move on to their contacts. Training montage inter-cut with accidentally in love. Eventually they encounter the Ghostfacers, but by then they’ve been around enough to get that these guys are kind of ridiculous. In this splinter universe, the Supernatural book series still exists. This is where Harry and Ed get all their ghost-battling ideas. They’re the kind of fans that talk about the characters like they’re real, but also talk about them as though their existence is a great injustice wrought upon the universe (yanno, Tumblr). They also think that Smith & Wesson have the stupidest, most obvious fake names ever. (Eventually S&W read the books, and Sam is subjected to endless teasing for his “brother” dreams, because Dean assumes he’d read them at one point, or his sister had fangirled at him and it became internalized.) Ed does help them though. He gives them the final push that gets them together, telling them about what happened between him and Corbett.
Sam and Dean are happily together for months, before the inevitable meeting of the families. They went to Sam’s family first, because Dean is insecure as ever. They don’t tell the Moores about hunting, but his family’s too glad to know he’s alright after Madison apparently committed suicide. (There was an investigation which turned up too much contradictory information to arrest Sam, but it was a near thing. Luckily, Dean Smith is smart enough [and anal enough] to insist on gloves and other protective measures, and the hunters they were working with were good at covering their tracks. Sadly, Madison was assumed to have had a mental illness, which, in addition to certain evidence in her house, pointed towards her having killed several people in the city before finally killing herself.) In their relief, the family don’t think anything about Sam having found a boyfriend named Dean, who may look just the tiniest bit like him. Dean learns about Sam’s adoption, and it sits a little uneasily with him.
The meeting with the Smiths goes a little differently. For one thing, Bobby and Ellen are a little more rough than Sam was expecting of neat, proper business!Dean. For another, there were the vampires.
Remember that bit at the end of Lost Boys, where Grandpa goes, “One thing about living in Santa Carla I never could stomach…all the damn vampires!” ?
Yeah, it’s kinda like that. Only with Ellen and Bobby, so it’s 1000x better.
Poor Dean. His life is a lie! It makes him feel a little better that Jo had no clue either. It also explains the copious amount of venison that he’s had to haul home over the years, and why his sister is so scarily good with a knife.
On top of that revelation, there’s the small matter of learning that he was adopted too. Luckily he’s internalized the ideal of “Family don’t end in blood.” However, the Smiths never knew that Dean had a brother, so that one’s staved off for a bit. Missouri knew Dean as a Winchester, that’s what she called him, and that’s what she wrote on the papers. She knew John was a righteous man who took the fall for a crime he didn’t commit.
They stay for a few months and train up a bit less haphazardly at Bobby and Ellen’s. Of course Jo insists on learning the trade too. Bobby and Ellen despair, but they privately admit to themselves that they knew they could never really leave the life. They were lucky enough to keep their kids safe until they could make the choice for themselves. This doesn’t mean Ellen will go easy on them, or that Bobby won’t make them memorize half his hidden library. Dean and Sam have come up with a few new and interesting ways to do things. Some are cribbed from the Supernatural series, some are just their own brand of awesome.
Meanwhile, Dean’s been having flashbacks that Sam seems to be picking up on with his Medium routine. Eventually, Dean’s need to find out what happened to him grows past the breaking point. He and Sam track down Missouri (Sam thought the Moores meant that he came from that state), and then the whole mess spills out. At first, Missouri tries not to say too much to ease them into the information, but the townspeople and the library archives are enough to get the whole picture.
After they confront her and get the whole truth, they are a bit traumatized. Dean calls it off before Sam can, instituting a no sex rule and trying to cultivate a brotherly relationship instead. Both are miserable for a long time. They’re reluctant to return to the Smiths’, since they’ll immediately know that something’s wrong. They don’t count on Jo taking it upon herself to track them down and drag them back. She definitely know that’s something’s up, and since Dean can’t keep anything from her, she knows the deal halfway back to the house. She tries to talk some sense into them. [You didn’t know, it’s alright, I still love you both, hey it’s legal for first cousins to marry here and at least you won’t be having any mutant babies?] Unfortunately, it doesn’t do much good before they arrive (even though Jo contrives to have an extra day’s stopover to give them some time).
Of course Bobby and Ellen suss that there’s something wrong as soon as they walk in. Dean tries to pass it off by telling them about his original parents, including Missouri’s doubts, but Sam gets pissy and stomps out to the guest room. Bobby gets defensive, saying that Sam shouldn’t be so angry about something like that, that Dean had no control over what his biological father may or may not have done. Ellen catches Dean and Jo’s shared look and makes them tell her the rest. Dean can barely get out that Sam is his brother. (To which Bobby says, “BALLS!”)
Afterwards, there is a consternated silence. [Sam, who really is too quiet for someone his size, lurks in a nearby room, listening with a heavy heart.] Finally, Ellen asks whether Sam flipped out and called Them off. Dean denies that, explaining his reasoning (sounding desperate to believe what he’s saying). His family doesn’t look convinced. In fact, they look kind of pitying, which is the worst. He really wishes he had Sam’s support in this, but it’s obvious that Sam wants nothing to do with him. When he says as much, Sam bursts forward and tells him that Of course he does, the idiot, he’s not in this just for the sex, that he loves Dean regardless and if Dean wanted to never do it again, well he’d not 100% okay with it, because they were good for eachother, really REALLY good, but he doesn’t ever want another partner, and if he had to have anyone as his brother, he’s glad it was Dean even if it means he can never have him again.
Which, yeah, embarrassing outpouring in front of the ‘rents, but it kinda soothed some ruffled feathers.
The tension eased, the two decide to investigate what Missouri told them about John’s case, which slowly leads along a road to the not-apocalypse…
Along the way, Dean and Sam still have a bit of a strained relationship. They can’t seem to fall into the brotherly roles after they’ve been something more. The ust builds for a while, even as they both try to hook up with other people on their travels. Eventually they stop trying and just come together naturally again.
Yes, I have headcanons for ALL the offshoot universes. (Aside from End-verse, because I don’t like to think of that one much.) Maybe not all as epic as this, but still.