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In a parallel universe, Leonard McCoy was the chief medical officer of the USS Enterprise in the 23rd century.
On one occasion, the Eleventh Doctor recalled memories of his fourth incarnation meeting up with the command crew of the USS Enterprise, including McCoy, to combat a Cyberman invasion of Aprilia III. (COMIC: Assimilation²)
Other references
A fictional character named Dr McCoy appeared in the science fiction television series Star Trek in the Doctor's universe. (PROSE: The Gallifrey Chronicles)
The Tenth Doctor briefly adopted the alias of "Dr McCoy" to Donna Noble's "Captain Kirk" when dealing with a group of soldiers. (AUDIO: Pest Control)
Behind the scenes
The mention of Dr McCoy in The Gallifrey Chronicles treats him as a fictional character (as do, implicitly, other references to Star Trek and Star Trek: The Next Generation in Doctor Who stories). Assimilation², of course, treats him as a "real" individual. Reconciling these diegetic levels is an exercise best left to the reader.
Assimilation² depicts McCoy with the likeness of actor DeForest Kelley, who originally portrayed him in Star Trek.