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Croats first appear in season two of the show when Sam and Dean go to a town in Oregon because Sam had a foreshadow of Dean killing somebody. The town became increasingly aggressive when Sam and Dean found themselves locked in and aggressive humans, Croats, guarding the exits. The number of Croats soon grew. People were dragged from their houses and infected or killed. The survivors made it to the police center and soon found the whole town abandoned.
The cause of this was found through Sam's blood when he was infected, the doctor said it was a virus, but she found sulfur in the bloodstream.
It turned out one of the other doctors was possessed by a demon and he contacted Azazel and said that "The Winchester boy is immune."
In the Apocalypse, the Croats were back, because it was the end game of Lucifer. Lucifer was intending to use Pestilence to spread the Croatoan virus all round Earth and infect humanity making himself an army of Croats.
When Dean got thrown into an alternate future, where Lucifer had won and the Croats were everywhere, he learned the virus started in 2012 and infected humanity. By 2014, the virus had reached Australia. The Croats were surrounding Lucifer, and acted as his henchmen. Dean had to evade them to get to Lucifer.
Although this future never happened, when Dean, Sam and Castiel hunted down Pestilence, they blew up the warehouse which had Croatoan virus test tubes in. Some workers had become Croats already and attacked them but they managed to kill these Croats and escape.