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Multiple realities
(covers information from several alternate timelines)
For the comic, please see Bones (comic).

Bones was a nickname for Doctor Leonard McCoy in multiple realities.

In the prime reality, Bones was short for "Sawbones"; this long version was used by James T. Kirk only rarely, usually using the shortened version "Bones" 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")

After watching a recording by the presumed-dead Kirk in 2268, Spock used the nickname by telling McCoy "Forget it, Bones", although he called it something Kirk would have said. (TOS: "The Tholian Web")

In the alternate reality, James T. Kirk referred 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)

The use of "Bones" originates with the term "sawbones" in 19th century American medicine where military doctors, especially surgeons, were called "sawbones" because of all the amputations they had to perform during the Civil War. The nickname appeared in Gene Roddenberry's original Star Trek pitch as the nickname for Philip Boyce, but was never used in "The Cage".
According to J.J. Abrams in his DVD commentary, the line explaining the nickname in the alternate reality was not scripted - Karl Urban, a Trek fan long before being cast as the doctor, thought of it while filming the scene.