When Dr. McCoy grumbles once too often about the way the "U.S.S. Enterprise" TM ought to be run, Captain Kirk decides to leave the doctor in command while he oversees a routine 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 captain, McCoy comes under pressure from Starfleet to resolve the situation immediately. Matters go from bad to worse when 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.