Sounds a lot like Who's Afraid of the Dark? by lukinha_jesus on Ao3.

Summary: It should have been just another birthday, but it wasn't. When Sam disappears mysteriously, John, Dean and Bobby team up to start a desperate search for him. Meanwhile, Sam wakes up in a strange, cold room, where no one talks to him, although he knows he's being watched. He's just a boy, and when things go terribly wrong, can Dean help him survive the darkness that creeps through his skin and nestles in his bones? This is a story of great darkness and pain, but also of great love and comfort.