In the Original Series episode "The Conscience of the King", Kodos, known as Kodos the Executioner, has been the governor of the Tarsus IV colony. He ordered the execution of 4000 colonists, and only nine survivors (including Captain Kirk) were able to identify him. Kodos had gone into hiding as the actor Anton Karidian. Several of the surviving witnesses died under mysterious circumstances, presumably as part of a scheme to protect Kodos's identity.

My question is this: How would killing all the eyewitnesses protect Kodos's identity? Kodos had been a planetary governor, hardly an obscure figure. It stands to reason that there would be plenty of photographs available to just about anyone in the Federation. In fact, Kirk is able to retrieve a photo of Kodos (and one of Karidian) from the Enterprise computer. His appearance had changed in the intervening 20 years, but anyone who had seen photographs of Kodos and Karidian should at least suspect that they're the same person. (Facial recognition software should turn that suspicion into a near certainty, but that probably wouldn't have been anticipated when the episode was written in 1966.)

For a modern parallel, imagine Osama bin Laden trying to hide in plain sight as a touring actor. One wouldn't have to have been an eyewitness to recognize him.

My guess is that it's simply a plot hole, but is there an in-universe explanation?

One explanation that occurred to me is that (spoiler):

his daugher Lenore, who was the one killing the witnesses, was not entirely sane, and she therefore might merely have thought that doing so would protect her father.

But all the characters involved, particularly both Kirk and Spock, seemed to accept that killing the witnesses made sense.

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    His appearance had changed considerably but I suspect the idea was that someone who'd met him would be able to discern him from his mannerisms and speech patterns. Also, there's a pretty reasonable chance that he's just plain mad. – Valorum Dec 30 '14 at 1:58
  • I don't have an answer, but this, to me, is just about the weakest plot point in all of Star Trek. As a young teen, I loved this episode. For some reason I didn't see it for many decades and finally saw it as an adult and couldn't believe all the plot holes in it. – Tango Dec 30 '14 at 2:41
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    Also, you wisely point out what many skip: the issue of facial recognition software working, but was not even conceived of in 1966. You can also add DNA testing to that, too. We do need to remember the time when a work was created. – Tango Dec 30 '14 at 2:43
  • If we're going to be realistic about it, we can reasonably predict that in the 23rd century, cosmetic surgery that can render him completely unrecognizable will come in a pill. Remember that this is Star Trek, which is defined as much by what the future doesn't have, as by what it does. – Beta Dec 30 '14 at 4:07
  • @Beta: Sure -- but we saw side-by-side photos of Kodos and Karidian, and they look like the same person 20 years apart. – Keith Thompson Dec 30 '14 at 4:41

To make a case against Karidian you can't just compare two photographs and say "that's the guy." A photographic likeness is enough to raise suspicion, but you can't pin the murder of 4,000 people on someone based on a photograph alone. You need first-hand testimony from witnesses who can put Karidian at the scene giving the execution orders. Without witnesses there may not have even been a trial.

As for how Kodos/Karidian could have evaded notice, consider that Radovan Karadžić evaded capture for well over a decade despite being the subject of an international manhunt. He did it by laying low for a time and then emerging with heavy facial hair and other appearance changes sufficient to allow him to move freely and work.

Kodos faked his own death, so there was no manhunt; it's hard to see what you're not looking for. Kodos was a planetary governor, but the planet had a population of only around eight thousand before the massacre. Kodos was more like the mayor of a small town than a planetary leader as we would think of one. I grew up in a small town and I can't remember the face of the mayor from twenty years ago.

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    To be fair, I doubt your mayor murdered half the town's population. That might have sharpened your memory somewhat. – James Sheridan Dec 31 '14 at 5:42

It's possible -- and I need to recheck the episode-- that the actual execution occurred outside of recorded media, even of the time, so what is not needed is witnesses to whether Karidian is Kodos (photo tech and other ID tech of the future can do that) but as to whether he ordered/conducted the executions. If I recall correctly, when Kirk has Karidian recite the execution order, it is an order Kirk drew from memory as an eye/ear witness and not from record.

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