The USS Enterprise, badly damaged from a recent encounter with a severe ion storm and reporting the death of an officer, arrived at Starbase 11 on stardate 2947.3, forcing Stone to delay scheduled repairs on the USS Intrepid.
That disruption to his starbase's routine was quickly eclipsed after Stone found a discrepancy between Captain James T. Kirk's deposition regarding the death of Lieutenant Commander Benjamin Finney, and a significantly different computer record of the incident. Stone entertained a number of reasons why Kirk might have killed Finney, from negligence to malice. For a moment, Stone was willing to sweep the incident aside for the good of the service, by offering Kirk a permanent ground assignment. Incensed by the accusation, Kirk maintained the error was in the logs and demanded his name be cleared.
Stone convened and served as the President of the Court in the first general court martial of a Starfleet captain in the history of the service. The trial proceeded smoothly until the investigation of Spock suggested tampering on the Enterprise computers. Stone accepted defense attorney Cogley's suggestion that the court re-convene aboard the Enterprise. Confirmation of Spock's suspicions led to the revelation that Finney was indeed alive and still aboard the ship.
After Finney sabotaged the Enterprise and she began to lose orbit, Stone refused to adjourn to the starbase, and shared the risks the starship's crew faced. From the bridge, Stone and the court officers heard the "testimony" of Finney by monitoring his confrontation with Kirk. Once Kirk had defeated Finney and restored the ship's orbit, Stone dismissed the court. (TOS: "Court Martial")
In the novel Vulcan!, by author Kathleen Sky, Stone's first name is established as David. Cloak differs and calls him Aaron Stone. The comic book story "Action of the Tiger" indicates he was later promoted to admiral.