A lot of people believe that it's Castiel, who's afraid of thunderstorms. Mostly they say, it's because it reminds him of his brothers and god all the times they fought.
But actually it's Dean.
Castiel is being hunted by rogue angels, his grace is fading. He has avoided going to the brothers because of Dean's condition and he doesn't want to call for help from Heaven. Seriously injured and outnumbered he's forced to go to the one place he can be safe but what he wants from Sam and Dean is not what they think.