Kirk leaves McCoy in command of the Enterprise for the first time while he beams down to broker Federation membership for the planet Flyspeck — and then vanishes, apparently lost in a time stream one of Flyspeck's native species doesn't experience the way everyone else does. With Klingons showing up to press their own claim to the planet and regulations forbidding him from just handing the conn to Spock, McCoy has to run a starship he never wanted while hunting for a captain stuck outside linear time.
Summary by Loreful, from public sources