I read a fic about a year back, I think it was most likely on AO3. I'm 90% sure it was Blair/Jim, or at least tagged as such.
Blair and Jim were fighting, Jim pushed Blair into a wall (?), before Blair left. Unbeknownst to Jim at that time, Blair had sustained a fairly serious head injury from the fight. Blair was then kidnapped by someone.
During the subsequent hunt for Blair by the police department, I think there were a few references to Jim having worked out that Blair was badly injured by him, and the Captain deliberately avoiding questioning him too closely because it would mean pulling him from the case.
Blair managed to escape at some point (from the boot of a car I think), but he was injured further (shot?). The place they'd took him too was surrounded by an electric fence, and Blair ended up deliberately setting it off so that the authorities were alerted.
Any help would be much appreciated. This one's driving me nuts and I can't track it down.
Cheers.ETA: Found, thanks to soxendom. It's Quiet Desperation by Arianna.