Nearly a half century of watching this episode (taking the odd toilet break occasionally), and I'm no closer, really, to figuring out what the hell was supposed to be going on at the end. I thought I had it once, but no. Plenty of episodes have the odd detail that makes no sense , fine, dead lines were looming, mistakes don't get fixed, no time. . . But here we're talking about the culmination of the story, what it's all leading up to. They must have at least thought it made some sense.
Alright, we're thrown the "fact" that any use of power disturbs the unstable space. The danger? Either they'd be lost in the other universe, or they'd screw up making contact with Kirk. The former as it turned out I guess. Fine, I don't need to know why any use of power is bad. I guess.
The Tholians finish their web. Its purpose? A great big transporter to send the Enterprise to some secure place as a captured ship. I think.
So.. . web powers up. Though the Ent is meant to vanish, right when it's supposed to, it vanishes to someplace else. Presumably it's Kirk's private universe where the Defiant is, because they slipped through as the Defiant did. But not really. The Enterprise wasn't dissolving. The Defiant wasn't powering up when it went, either. So more than one way to cross over. Confusing.
So it's a black place without stars. If they'd detected Kirk and the Defiant in this void and beamed him aboard, fine, then they'd have to figure out some way to get back out of the empty universe.
Instead, they're in the black place a few seconds, then re-appear in normal space, somewhere away from the Web . It's only then that they see Kirk, who conveniently takes center stage right in front of them, right in the middle of the viewscreen. They have him there because he was caught in a transporter beam (when?) and carried along by it, to the regular universe. Did someone somehow forget to turn off the transporter after their last attempt? It caught him in the beam, but they didn't know? I'd almost say they were thinking of a tractor beam.
Spock "explains" : "By utilizing ship 's power we have been thrown clear of it ." Clear of the Web. How did they get back? Why another point in space?
Well, I'm done.