Here are a couple that I remember off the top of my head.
Treasure (http://archiveofourown.org/works/402918/chapters/664221) by sonofbiscuit - It’s 2018 and the human race is almost extinct, wiped out by a mutant threat not even the angels saw coming. Sam and Dean live on a military compound, one of the only human communities left still fighting for survival. Dean is one of the military leaders, dedicated to wasting as many of the mutants he can, while Sam, permanently injured and confined to the base, is desperately searching for the answer that will save what’s left of humanity, and finally bring both boys the peace they crave.
All Along the Watchtower (http://archiveofourown.org/works/181729/chapters/267268) by leonidaslion - When the world explodes in a heatless, formless flare of red light, Dean isn’t awake to see it.
There's another one that I know of but I have to look it up when I get home. :)
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Treasure (http://archiveofourown.org/works/402918/chapters/664221) by sonofbiscuit - It’s 2018 and the human race is almost extinct, wiped out by a mutant threat not even the angels saw coming. Sam and Dean live on a military compound, one of the only human communities left still fighting for survival. Dean is one of the military leaders, dedicated to wasting as many of the mutants he can, while Sam, permanently injured and confined to the base, is desperately searching for the answer that will save what’s left of humanity, and finally bring both boys the peace they crave.
All Along the Watchtower (http://archiveofourown.org/works/181729/chapters/267268) by leonidaslion - When the world explodes in a heatless, formless flare of red light, Dean isn’t awake to see it.
There's another one that I know of but I have to look it up when I get home. :)