Doctor's Orders (Star Trek: The Original Series #50 by Diane Duane
Blurb from Goodreads:
When Dr. McCoy grumbles once too often about the way the U.S.S. Enterprise™ ought to be run, Captain Kirk decides to leave the doctor in command while he oversees a rountine diplomatic mission. Kirk beams down to a strange planet nicknamed "Flyspeck" to negotiate its admission into the Federation, leaving Dr. McCoy to enjoy his new authority.
However, the doctor soon learns that command is a double-edged sword when Kirk disappears without a trace. Desperately trying to locate his catain, McCoy comes under pressure from Starfleet to resolve the situation immediately. Matters go from bad to worsewhen the Klingons arrive and stake their own claim on Flyspeck.
Then another, more deadly power threatens them all, and suddenly Dr. McCoy and the Starship Enterprise find themselves pitted against an alien fleet in a battle they have no hope of winning.
A surprisingly philosophical book that brings many questions to mind and causes a change in perception of the very world. The world of three species was an intriguing surprise for the Enterprise crew and the reader. The amount of creativity shown by the author through the very creation and fleshing out of such alien beings and thoughts was wonderful, the added time element positively mind-bending.
I in particular loved the switching of view as it pertained to being captain of a starship a wonderful look into the minds of the characters. The opportunity to read of Dr. McCoy in a command position so changed from his sickbay was beautiful.