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An autopsy, also called a post-mortem examination, is a procedure in which a deceased organism undergoes a thorough examination to determine how, when, and why the organism died, as well as to determine if there are any pre-existing conditions which may have led to death.
After a Suliban force boarded the Enterprise (NX-01) and kidnapped Klaang, Doctor Phlox had an opportunity to autopsy a Suliban corpse. The autopsy revealed that Suliban in question was quite different internally than a regular Suliban. (ENT episode: "Broken Bow")
When in orbit of Alfa 177, the USS Enterprise suffered a transporter malfunction which caused an Alfan canine and Captain James T. Kirk to be split in two. In each case, one being behaved in a positive manner, while the other only exhibited negative behavior. After the transporter was repaired, the reintegration process was tested by having the canine go through the transporter, but the animal died in the process. Doctor Leonard McCoy ordered an autopsy, which revealed the animal had died because of the shock of reintegration. (TOS episode: "The Enemy Within")
Following the death of Crewman Scott Darnell on planet M-113, Dr. McCoy had his body beamed back up to the Enterprise so that he could perform an autopsy. Unfortunately, McCoy was unable to determine the cause of death or confirm Nancy Crater's account that Darnell had ingested a piece of Borgia root. (TOS novelization: The Man Trap)
While on a Romulan ship, Commander Spock used a neck pinch against Captain Kirk to simulate death. The Romulans allowed Doctor McCoy to take Kirk's body back to the Enterprise rather than beginning an autopsy, which would've been fatal to Captain Kirk. (TOS episode: "The Enterprise Incident")
After a Frenni vessel commandeered by the Ravens made a kamikaze run on the Enterprise, the Enterprise crew was able to bring aboard a Raven corpse for Lieutenant Fraser to perform an autopsy upon. From this autopsy, Fraser found that the alien - which was quickly dubbed a Raven - had never been encountered before by the Federation, and had a very unusual brain structure. After a second Raven attack on the Enterprise, more Raven corpses provided even more insight into Raven physiology. (TOS novel: Dreams of the Raven)
While many cultures permit an autopsy to be performed, some cultures do not. When Dr. Beverly Crusher wanted to perform an autopsy on Sev Maylor - the woman whom Ves Alkar claimed was his mother, Alkar cited cultural reasons for denying permission for an autopsy to be performed. However Alkar had forced Maylor to be a receptacle for his negative emotions, and he may have been lying about there being a cultural prohibition against post-mortems being performed to keep his secret from being exposed. Picard initially upheld this judgment, but when it became apparent that something was very wrong with Deanna Troi, Picard allowed the procedure to be done. The autopsy revealed that the Maylor was not 93 years old, but was only in her 30s. Analysis of the woman's genetic structure revealed that whoever Maylor was, she was in no way related to Alkar, thus exposing him. (TNG episode: "Man of the People")
Ferengi culture also did not permit autopsies to be performed before the deceased was vacuum dessicated. When the scientist Dr. Reyga was murdered on board the USS Enterprise-D, Doctor Crusher violated this cultural prohibition, as well the orders of Captain Jean-Luc Picard to perform an autopsy. When she admitted this to Captain Picard, Crusher was relieved of duty and was due to attend a hearing at Starfleet Medical to determine what action would be taken. Doctor Crusher was later able to prove that Reyga was murdered, and was ultimately not punished for performing the autopsy on Reyga. (TNG episode: "Suspicions")
In the past, an autopsy would involve the physical dissection of a person, in which the person's body would be opened, and the organs would be removed and thoroughly examined. By the 24th century, non invasive methods were developed that generally removed the need for the more gruesome aspects of an autopsy. (TNG episode: "Suspicions"; TNG novel: Imzadi)
In an alternate timeline in which Deanna Troi had died in 2368, Admiral William T. Riker would later order an autopsy to be performed on Troi 40 years after her death - which revealed that she was poisoned with a substance which wasn't generally available at the time of her death. It was later revealed that the timeline had been altered, and the timeline was later prevented from occurring when Riker traveled back in time to prevent Troi's death. (TNG novel: Imzadi)
Autopsies conducted on Jem'Hadar by Starfleet in and after the Dominion War revealed some Jem'Hadar over the age of ten developed the ability to produce small amounts of ketracel-white themselves. (DS9 novel: Avatar, Book Two)