The tale I'm looking for is a coda to ITGPSW. I'm fairly certain it was a comment fic. I could well be wrong though, so.
After Sam  kills Samhain. He has a blasting head-ache which he thinks is from  working his power. Turns out he has menengitis.. I have looked high and low for this and I'm fairly certain I am going to feel like an idiot when i find it becusue I should recognize who the author is. Sadly I do not remember author or title

ETA: I also remember that Sam didn't tell Dean  that he was feeling really ill because he assumed that Dean was completely disgusted and angry with him. It was pretty angsty.

Son of ETA: FOUND link in comments