There are a few other things that are seldom discussed, but have always bothered me about the film.

* SPOILER WARNING *

The Issues

First of all, why don't the crew of Reliant know all about Khan Noonian Singh before they enter the Ceti Alpha system? Either they are total incompetents, or the information is not in the Reliant's computer banks. Since they are a trained Starfleet crew, we assume it must be the latter. And since we can safely assume Spock logged it at the time, it must have been deleted later.

Second, even granting the lack of information about Khan, how could Reliant enter a known and charted system and miss the evidence of the explosion of Ceti Alpha Six, and the wrong orbit of Ceti Alpha Five (which they mistake for Six somehow). How does Reliant's database not alert them to the problem? It must contain data that was updated or altered after Ceti Alpha Six exploded.

Third, how could Spock allow the crew of the Botany Bay to be marooned on a planet with such an unstable planet as Ceti Alpha Six a neighbor? Well, he wouldn't. There's just no way Spock misses something like that. Remember:

KHAN: Ceti Alpha Six exploded six months after we were left here.

Not much time. So the instability developed suddenly, shortly after Enterprise left the system.

So what's up? Patience. All will be revealed shortly...

Another mystery: When the Enterprise boarding party finds Terrell and Chekov aboard Regula One the following conversation about Khan occurs:

TERRELL: ... He's completely mad, Admiral. He blames you for the death of his wife.

KIRK: I know what he blames me for.

Now, how does Kirk know this? He's had exactly one conversation with Khan, since he left him on Ceti Alpha Five at the end of Space Seed, which was during the recent space battle. The closest they got to the topic was this:

KIRK: What is the meaning of this attack? ...

KHAN: Surely I have made my meaning plain. I mean to avenge myself upon you, Admiral.
But I wanted you to know first who it was who had beaten you!

That's it. So how does Kirk know what Khan blames him for? Khan didn't tell him, ergo he knew already. And how did he know already?

Well, we have one more piece of data. Kirk, unbeknownst to us all, is a hacker. When they're in the Genesis cave Kirk explains to Saavik how he came to be the one and only Starfleet cadet to beat the Kobayashi Maru scenario.

KIRK: I reprogrammed the simulation so it was possible to rescue the ship.

And since no one has else ever succeeded in doing this, presumably it was a fairly difficult hack.

The Cold Hard Facts

So let's look at our facts and hypotheses:

  • Reliant's computer banks have no data on Khan or the Botany Bay crew. It was therefore deleted.
  • Reliant's computer banks have updated data on the Ceti Alpha system, but data which is not complete (misnumbered planets, for example).
  • Ceti Alpha Six exploded shortly after Enterprise's visit, and this was never discovered.
  • Kirk knows what Khan blames him for.
  • Kirk is a hacker of no mean ability.
What does this tell us? Simply this:

The Conspiracy Theory

Kirk secretly arranged for Ceti Alpha Six to be blown up, thus changing Ceti Alpha Five from an idyllic world into a hell hole. ("Try to asphyxiate me, will you, Khan?"). He later uses his position in the Starfleet Admiralty to alter the Starfleet database to remove all record of the crew of the Botany Bay and to hide the changes to the Ceti Alpha system from casual discovery.

KHAN: Admiral Kirk never bothered to check on our progress.

That's where Khan was wrong. Kirk checked up, all right. He knew. He enjoyed every minute of the suffering of the Botany Bay's crew. It was only a fluke that Kirk did not know of the Reliant's mission so that he could divert them.

Summary

The actions of James T. Kirk in this case are clear. He deliberately caused cruel and unusual punishment to be inflicted on the crew of Botany Bay and is indirectly responsible for all harmful events stemming from Reliant's contact with Khan.

Note: To the best of my knowledge, this theory is my own, original, paranoid, psychotic idea.