Commodore Mendez shows Captain Kirk the secret orders from Star Fleet Command. There, in big letters on paper, is the mention that the Enterprise visited Talos IV once. It then reveals that Captain Pike and Science Officer Spock were there. You wonder why, of 203 people on board, the signing Admiral would specifically only mention those two. Let us forget, for a moment, that there was little Star Trek precedent for anything, since this was only the sixteenth episode of all. Even then, it would make sense to mention the captain only — not the science officer for any specific reason. But, lo and behold, what an incredible coincidence: these are the same two characters who are deeply involved in the plot here!
Star Fleet’s orders are cheesy to the point of being silly, reading like a child’s arbitrary play rules. No explanation is given of why no one is allowed to go near Talos IV. In simple, arbitrary words, there is only passing mention that Pike and Spock have recommended the ban. Because they say so, the Admiral forbids everyone else?! This is a death-threat matter and no elaboration is offered except authority? Furthermore, the prohibition seems to be well known, but the only top-secret information to be added is that the Enterprise has been there once and two officers (the same two from this one episode, lest we forget) recommend fencing the planet off…? What to say of the other 201 souls who were also there? Are they forbidden from speaking? Are they omitted from the records for any reason? Does Star Fleet sweep their knowledge under the rug, or are they the ones allowed to talk? Can anyone ask them? Is it a secret that they were ever there?… Why mention the science officer but not the first officer or the yeoman, who were more intimately involved with the developments there? Questions, questions… It would have been better if NOTHING was said than saying that ridiculous, childish little.
Let us assume for a moment that you are a computer technician. Let us assume that you come into your workshop and you find your superior officer, a man twelve times as strong as you, tampering with the equipment that you are responsible for. What do you do? (1) You rush off to intercom the starbase commanding officer about the breach of security; (2) you politely ask what is going on, then rush off in panic; (3) you try to stop your Hulk-strong superior officer from tampering. If you chose (3), you are the stupid technician who was brushed aside by Spock as if he were a stupid ragdoll.
Also, Mendez and Kirk start chasing the Enterprise on a shuttlecraft. How hopeless can one be? It has already been stated that the Starship was running at maximum warp (which, by the way, is necessary for Spock to increase his chances of attaining his goals here). The Enterprise is reputedly one of the fastest known ships. Certainly a shuttlecraft would be no match even to feign pursuit.
Moreover: it makes no sense that Commodore Mendez, in charge of a whole planetside Starbase, would leave on a shuttlecraft (of all vehicles) with another command-ranking officer, especially on a foolish errand such as this! Maybe we could accept his leaving on another Starship — that could be a match, making for interesting starship-chasing scenes –, but not a sad contraption as this.
When Spock outright lies to everyone on board and simulates a secret mission, McCoy and the bridge crew are already somewhat dumbfounded. When he later just up and turns command to the first officer that happens to be sitting nearby, surrendering to McCoy and almost self-escorting himself off the bridge, it is genuinely funny to see everyone’s “WTF?!?!?!” face, including Uhura and McCoy. They were confused before; now they simply cannot judge whether he is lying again: if now he says that he was lying, can they trust him to be telling the truth this time? And what is going on then? There simply is no frame of reference for one to cling to.
A spoiler for Part II (but, 46 years on, I assume that anyone not to have seen Part II deserves to be spoiled): it is to Roddenberry’s credit that he explained the high-quality transmission as coming from Talos IV. In point of fact, he addressed it directly when the characters themselves stated that it was impossible that it would have been filmed at the time. This addresses a classical concern up front; namely, the old fans’ complaint that there would have been no omniscient camera floating in space, visiting the captain’s quarters etc. and that the privileged audience’s view would make no sense.