On Natural Instincts, the story of Supernatural starts after the 5th season finale and very loosely follows the seasons after that.
The Great Revelation
It was over.
The big apocalypse was over. Everything had led up to that one moment, the moment when Sam said “yes,” the moment where Sam threw himself into the pit – trapping Lucifer where he belonged - the moment where Dean lost his brother. Earlier, Sam had asked Dean to let him go if things went as planned – to not try and fish him out of Hell. Dean kept that promise. He went to Ben and Lisa’s and had dinner there. But on the TV that evening was news of the Great Revelation (TGR). The time of TGR seemed to coincide with Lucifer’s trip back to Hell.
- Dean: What the hell’s going on here, Bobby?
- Bobby: You’ve seen the news. You already know what’s going on. Something’s going on, I’ve been calling around. No one knows more than what’s on the news.
- Dean: Friggin’ great. The vampires are going crazy and a bunch of people are going to die trying to kill them.
Dean knew that things would get crazy in the supernatural world but for now, he was content on living his life – a normal life, with his new family. No more hunting, no more getting involved with apocalyptic battles. Dean
was done. That isn't to say that it wasn't hard - watching the whole world change before his eyes and choosing not to do a thing about it. The world now knew vampires existed and were actually warming up to the idea of integrating them in society. But Dean kept himself at bay for a few months. That is, until later, when the Russell incident happened. Dean then took up hunting once again to protect Lisa and Ben.
- Dean: Shit. These things are really starting to get stupid.
- Lisa: What’s going to happen?
- Dean: Nothing. Nothing is going to happen to you, Ben, or anyone else that doesn’t get involved. I can make arrangements for you and Ben. There are other hunters, they’ll kick their asses. Simple.
- Lisa: You have to explain to me what’s going on.
- Dean: I don’t even know if I can.
Sam's Return
Sometime around then, Sam ended up inexplicably in NYC, dragged out of hell. He had no memory of what happened, why it happened or who did it. But he knew one thing, Lucifer was a free agent – he could feel it. Something just wasn’t right.
The first thing he did was call Dean, after numerous tries (often because people didn't believe it was him), Sam convinced Dean that it was really him and that they were all in big trouble. The fight with Lucifer was not over. Dean knew he had to leave to see his brother, fortunately Lisa was glad for him to go knowing that being a
hunter was who he was. She knew that Sam would be the end of her relationship with Dean and she told him to go and find Sam, to be a hunter knowing that was what made him happy. Dean made the decision; he would go to NYC to reunite with his brother.
When he did, after a while, he knew something was up with Sam. Sam refused to open up about what happened to him in Hell but whatever happened, it changed him. Dean still can not pinpoint if that change was for the better or for the worse, or what it meant of the both of them in this ongoing fight against Lucifer. In the meantime though, the brothers set up shop in a hotel, and continue to try and wrap their heads around the concept of 'vampire rights '...especially when the vampires were clearly trying to wipe out the human race. Perhaps thats just what hunters were for. That, or the world had really gone to hell.
Since then, Sam separated from Dean due to his lack of a soul.
War in Heaven
Meanwhile, there is a civil war in heaven and angel Raphael is right in the middle of it. Wanting the Winchesters on his side, he has resurrected 4 women that are a major part of the Winchester's lives: Jo, Anna, Bela, and Ellen. With all four of them in debt to Raphael for bringing them back to life, they are obligated to help Raphael get the brothers on his side.
Levianthans
Lucifer and Crowley tried to go after purgatory and end up releasing the Levianthans. The political climate of NYC certainly went through some changes when the Levianthans enacted their agenda. Dick Roman rose to the status of Senator and ended up mayor, launcing his food chain all over the city. Dean, Sam, Jo and a few others worked together - researched tirelessly - before confronting Dick Roman. In the battle to throw Dick back into purgatory (along with the rest of the leviathans) - Castiel, Dean, and another hunter named Gunn (from "Angel") were thrown into purgatory as well. Eventually they escaped.
Change of Events
For a long while, Dean had to deal with not having his brother around - but continued hunting. It was only until they were both confronted by Crowley that Sam ended up reunited with Dean. Crowley forced Sam to take back his soul, and this left him severely unstable. They didn't have much time to regroup , as the Leviathans had already made their mark and it was time to stop them.
After being successful in this, and with Dean back from purgatory - the brothers are now trying to find out a way to close the gates of hell for good.