Back on the good ship USS Topeka (SSN 754) during our '92-'93 WestPac/Arabian Gulf deployment, we had a last liberty call in Hobart, Tasmania -- in my opinion, the absolute best liberty port in the world, because the people genuinely liked American Sailors. We picked up a new crew member and headed towards home via the realm of the Golden Shellback. Since we had an ORSE scheduled prior to our return to port, we planned to spend the whole transit working up for the inspection. Unfortunately, the new crew member had brought aboard what we ended up dubbing the "Tasmanian Swine Flu" -- a really virulent form of the dreaded "double-header disease" (the one where you're puking and crapping liquid simultaneously and violently) and it spread through the crew quickly. We were lucky that we never ended up with only one person at a watchstation; it had you down for about three days, and about a third of the crew was off the watchbill with it at any time, but we always had enough people to stay port and starboard. Our CO, "He Who Must Not Be Named", somehow used his powers of Evil to stave off the disease until the deployment was over, at the cost of coming down with a 10 day version of it as soon as we returned to port.
What horrible / humorous epidemics have you experienced on a submarine?
