Female crew refuses to set foot in his office and all die of a Denebian Yeast Infection, leaving the ship vastly understaffed during a confrontation with the Romulans. Decides in first week on duty that the Prime Directive is too restrictive and narrow-minded. McCoy Argues with every suggestion offered him, alienates most of crew, sasses off to Starfleet. Suicide rate of Enterprise crew twelve times average.
Ship never leaves dock.
Tries to fire lawyers and act as own defense during court-martial. Knifed in prison by a Vulcan who very logically didn't want to take any more of his shit. Constantly tinkering with crew's innards, optimizing kidneys and routing pancreas enzyme flow through the hypothalamus. Health actually improves, but Scotty is the only one who understands everyone's internal layout, forcing all transfers and de-commissions to be declined. This proves astonishingly more useful than a traditional Science Officer, and all ship-board science stations are replaced with wet bars.