The Cottle subplot was a little contrived, mostly because we've seen this kind of thing before on Star Trek a million times. I did like that they were willing to avoid pulling a tidy cure out of nowhere by the end, though. Baltar's joke about Helo surviving everything was a nice touch, though knowing this show, it probably means he'll die from the infection next week.
EDIT: What was with the cutaway to Tyrol during the negotiation scene? It looked like he was digging something up, but they didn't show us what. Though that explains the title, I guess.