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In 2153, Captain Jonathan Archer ordered Doctor Phlox to perform an autopsy on a Xindi-Reptilian that had committed suicide after being captured while retrieving Rajiin from Enterprise NX-01. (ENT: "Rajiin")
In 2154, after the Enterprise encountered a crashed ship of dead Xindi-Insectoids, Archer wanted a complete autopsy from Phlox. The autopsy revealed that they had died not from the crash, but rather from suffocation after they transferred life support to their hatchery to save their children. (ENT: "Hatchery")
Shortly thereafter, T'Pol had a nightmare in which she and members of the Enterprise crew were watching the film Appointment with Danger. In the nightmare, Phlox did not truly believe that one of the characters in the film, a detective with a bow tie, had perished in a house fire since "the autopsy was inconclusive". (ENT: "Impulse")
Autopsies were conducted on the nine crew members of the USS Enterprise who were killed after the starship attempted to cross the galactic barrier. The results showed each crew member suffered neural damage, effectively "burning out" an area of the brain. This report was delivered to Captain James T. Kirk by Doctor Elizabeth Dehner. (TOS: "Where No Man Has Gone Before")
In 2266, Doctor Leonard McCoy performed an autopsy on Crewman Darnell. After an inconclusive result with the first autopsy, Captain Kirk ordered a second autopsy. Based on the findings of this autopsy, Dr. McCoy concluded that the crewman's body had been drained of salt, which lead to his death. This finding contradicted a story told by Nancy Crater that Darnell had unwillingly poisoned himself with an alkaloid poison found in the borgia plant. (TOS: "The Man Trap")
In 2267, Captain Kirk ordered Doctor McCoy to perform an autopsy on Thelev, whom Kirk had just been forced to kill. The autopsy revealed that Thelev was not an Andorian as he appeared, but was in fact an Orion. (TOS: "Journey to Babel")
In 2369, Doctor Beverly Crusher asked Captain Jean-Luc Picard to persuade Ambassador Ves Alkar to allow her to perform an autopsy on Sev Maylor, having rejected Crusher's initial request to do so under the claim that Lumerian custom forbids it. Although Picard initially refused since there was no proof that whatever had killed Maylor could after the crew of the USS Enterprise-D, he permitted Crusher to proceed after Deanna Troi began to suffer the same symptoms as Maylor. (TNG: "Man of the People")
Also in 2369, aboard the Enterprise-D, Doctor Crusher wished to do an autopsy on Ferengi doctor Reyga to prove her suspicion that Reyga was murdered. However, Reyga's family demanded that the body not be violated before they can perform the Ferengi death ritual. Despite this, and against the orders of Captain Picard, Dr. Crusher performed the autopsy. Although she initially found no evidence of foul play, further investigation proved Jo'Bril guilty of murder. (TNG: "Suspicions")
Doctor Bashir was about to perform an autopsy on Vedek Bareil Antos in 2371 after the Vedek was injured in a shuttle accident. The autopsy was delayed, however, when it was found that his nerves were still transmitting signals to his brain. Bareil died shortly thereafter. (DS9: "Life Support")
That same year, Chief Miles O'Brien was transported several hours into the future where he learned from Doctor Bashir that he had died from radiation affecting the basilar arteries in O'Brien's brain stem, information Bashir had acquired through an autopsy on O'Brien. Bashir offered to share the dead O'Brien's autopsy results with the O'Brien from the past, but the chief quickly refused. (DS9: "Visionary")