Ya gotta remember, 99.99% of the time, Kirk doesn't get bonked on the head and the transporters work just fine.
Yeah, their FTL communications and information exchange is a bit of a mystery. But the dangerous stuff from a nova (I don't think this one was a super nova but just a nova) is much slower than the light signals or other EM waves, so warp 1 ought to do it. Of course, there is probably subspace stuff coming off most everything that they use to detect stuff light years away and see it, etc., but in this case, I don't think anything too dangerous will be coming out at FTL speeds, so I think 3 hours to look around a place sensors say has no sapient life to threaten you, and the fact the ship and its systems are working just fine, doesn't seem too big a stretch.
There were heaps of episodes when Kirk couldn't beam up when he wanted and when he was captured or had some other reason he was trapped on the surface of some planet he did not want to be - Mirror Mirror, Bread and Circuses, The Omega Glory, Doomsday Machine, Mark of Gideon, Miri, Shore Leave, Squire of Gothos, etc - in fact probably every second episode.
In the episode "Dagger of the Mind," Kirk decides to stay "overnight" at the Tantalus facility with Dr. Noel.
I really could not see any good cause for him to do so. What tangible, plausible reason could there be? Adams showed himself to be perfectly normal and gracious. From all that transpired up to that point, he didn't give Kirk any cause for suspicion. The issues with Dr. Van Gelder checked out with McCoy.
On top of that, he decides to undertake first hand exposure to the Neural Neutralizer device, at the hands of Dr. Noel, who never had any experience with this device. Stupid. Why? Well, if Dr. Van Gelder was abused with this device, one would have to intentionally do it. So was he going to take a chance at risking his own sanity to see how far the device could be pushed?
Just a critical note on the episode... Dr. Adams must've been a functional lunatic. Did he really think he could kidnap Captain Kirk? Or perhaps brainwash him to do his bidding at remote distances? What's weird is that it was all predicated on Kirk a) deciding to stay overnight, and b) voluntarily (and without permission) taking the risk of experimenting with the Neural Neutralizer. What if Kirk and Noel decided to stay for just one day? Or... what if Kirk didn't bother to take any chance on experimenting with the device?
Lastly, the sort of "icing on the cake" for how weird this episode was... Kirk gives the "take us out of here, warp factor 1" command to Mr. Spock, not the helmsman. I don't think he ever does this again in other episodes. At least this episode did give us some decent entertainment with Morgan Woodward and Marianna Hill.
Kirk stayed overnight because for once he was paying attention to McCoys gut feel. Unlike ManTrap or Enemy Within.
But I don't understand Dr Adam's motivations either. He'd already covered up Van Gelder's "accident".
He just need to be cool. Kirk didn't have anything on him.
Say goodbye to Kirk and keep on with his wacky experiments.
Adams didn't seem to be motivated by galaxy domination. Maybe he panicked.