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(covers information from several alternate timelines)
In the prime reality, Bones is short for "Sawbones"; the term was used by James T. Kirk almost exclusively to refer to Leonard McCoy during their service together. (TOS: "The Man Trap", "A Piece of the Action"; Star Trek VI: The Undiscovered Country)
During a 2267 landing party mission on Pyris VII, Kirk made a special point to avoid calling McCoy "Bones", instead using the nickname "Doc", after finding themselves in shackles hanging alongside a skeleton. (TOS: "Catspaw")
In the alternate reality, James T. Kirk refers to Leonard McCoy as Bones because, as mentioned by the doctor the first time they met, all his ex-wife left him after their divorce was his bones. (Star Trek)