FOUND: Fire from a Busted Gun http://archiveofourown.org/works/524070/chapters/927353
This is another fic (or two, which had similar concepts), but Loki ends up in medical on the helicarrier because they realised he was being controlled or something. Hes delirious/injured/sick a lot of the time and freaks out, panics and hides from everyone. I beleive he also tries to hurt/kill himself.
Hopefully someone knows what fics im looking for. Thanks in advance!