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Seeing things from Khan's point of view...

I'd still argue that Starfleet at large was left in the dark, and that Kirk marooned Khan in secret

But if it's in the logs, it's not "secret" (and Kirk's logging it all is part of "Space Seed.")

That's not to say that Starfleet would broadcast that episode to everyone traveling to that system, but I think Kirk was pretty meticulous in his recording of the episode—Kirk may have sympathized with Khan to a degree, but that didn't mean he was willing to jeopardize his own career for him.

Keep in mind that in the "frontier"—be it "final" or American West of the 19th century—the military often was the de facto law in areas without formal civilian justice facilities. So it would be completely normal for a Starship Captain, out in the frontier, to dole out justice in a formal hearing. Starfleet most certainly would have accepted his edict in good faith, as long as he held a proper hearing and documented it as their regulations required.

Orren

Plus, as I said up thread, there is an Augment fear/bigotry in the Federation-- or rather mostly within Starfleet and humanity. The way they might have looked at it is that Kirk saved them some work and headaches (at the time) by marooning him on some backwater planet.

Or to think of it another way: Kahn was a classic leader. He was able to convince people to follow him, even a Starfleet officer (we'll leave out the fact that she just had the hot pants for a piece of living history). Stick Kahn on a penal planet and you're going to have a man that's going to raise up an army against you. Kahn was a cold blooded, smart, charamastic manipulator. Alive in a penal colony he would be dangerous, a risk. Dropped off on some world and forgotten about with only the most barist of necessities to live, he's just a note in a Captain's log.

It is entirely possible that Reliant was sent to the Ceti Alpha system to check up on Kahn and see if he was alive or dead. It was just dumb luck that Terrell and Co. were so bored that they were looking for any excuse to clear the planet for use with Genesis that they beamed down to check out something that most people would have written off as a sensor glitch (Which Chekov first thought).
 
Plus, as I said up thread, there is an Augment fear/bigotry in the Federation-- or rather mostly within Starfleet and humanity. The way they might have looked at it is that Kirk saved them some work and headaches (at the time) by marooning him on some backwater planet.

Doesn't sound convincing. After all, you yourself later say:

Alive in a penal colony he would be dangerous, a risk.

Now he's alive in a colony that isn't even penal. Nobody guards him. Nobody keeps him from repeating what he did the first time around: intercepting and hijacking a modern space transport while asleep in an immobile facility.

In "Space Seed", we couldn't have known yet that the Federation hates/fears people like Khan; the impression we got was that all Earthlings worship him, while Vulcans don't yet understand why but will eventually come to see things the Earthling way. In that context, it wouldn't have made much sense for Kirk to hide his dirty deed from his superiors. In that context, Kirk's act would indeed probably be seen as practical frontier justice - in the sense that Khan belonged in a jail, but Kirk didn't have a jail with him on his long voyage through the high seas, er, space, so an uninhabited island, er, planet, was the next best thing.

In the later context of Earth objecting to the Augments, though, Kirk's actions only make sense if seen as a rebellion against Starfleet, in Khan's favor.

As for Kirk's logs, or those of the other officers, they always were malleable. Secrets were recorded on them, then supposedly either locked up or erased. Apparently, the voiceovers were dictated on them afterwards, too. It would take some effort to falsify a flight recorder's visual output, but it could be done by a person with sufficient skill (records specialist Ben Finney, noted computer expert Spock) or a person with sufficient clearance (James Kirk, who would have been extremely unlikely to possess the skill). More personal records like dictated logs could apparently be modified at will, such as when Kirk is made to "forget" in "Requiem for Metusaleah", or when Spock and McCoy try to pull the wool over Kirk's eyes in "Tholian Web", etc.

It is entirely possible that Reliant was sent to the Ceti Alpha system to check up on Kahn and see if he was alive or dead.

You mean, without telling Terrell what his real mission was? That would be a summer repeat of "Space Seed", then - a starship stumbling onto Khan unawares. A 100% sure recipe for disaster. And how could that work, with Chekov aboard and knowing (even if not necessarily remembering) that Khan resided in the system?

Timo Saloniemi
 
Now he's alive in a colony that isn't even penal. Nobody guards him. Nobody keeps him from repeating what he did the first time around: intercepting and hijacking a modern space transport

But a normal penal colony would have regular visits by starships. There would be an opportunity for Khan to escape. Ceti Alpha was apparently not on the normal shipping lanes or anything like that, so if the crew of the Reliant hadn't screwed up and visited the place by accident, Khan would never have had a means of escape.
 
But the Botany Bay was no more on the route of regular traffic than Ceti Alpha was. Marooning Khan there would thus be no improvement from the law-enforcement, UFP-shipping-security point of view: lightning had stricken once, and could strike again.

A ship loitering into the Ceti Alpha system unawares would probably be an "irregular" vessel, thus likely a powerful exploration ship or warship - dangerous indeed if caught by Khan. And then we learn that just such a vessel enters that system, seemingly unawares, uninformed by Starfleet about what might be found there. So if Starfleet knew of Kirk's plan to maroon Khan, and approved of it (even if ex post facto), and then seemingly refused to release information about the marooning even to its own personnel, then Starfleet willingly created a situation of deadly risk.

If Starfleet didn't know, then only Kirk took the insane risk - which is logical in light of what we learned later, namely that most of the UFP hates and fears the Augments, as well as in light of what we learned originally, namely that Kirk, McCoy, Scotty and probably several other top officers of the Enterprise appreciate Khan for his abilities and achievements. Those who take risks like and help Khan; those who hate Khan are kept unaware of the risks; and eventually, disaster strikes again.

Timo Saloniemi
 
While it's a rather thin excuse, and I'm not going to claim otherwise, it's possible Kirk dropped a warning buoy in the system before Enterprise left...only for it to be destroyed when Ceti Alpha VI exploded.
 
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