Season 3 of Star Trek is a mixed bag, delivering some of the best episodes of the series, some of the worst, and also some of its weirdest. "That Which Survives" is hardly weird or bizarre in the conventional sense, but it is one of the more unusual episodes of the series, and very much a product of the strange and off-kilter sci-fi of the time. And you know what? I kinda love it for that.
The plot is simple; Kirk and a landing party investigate a planet that defies scientific explanation, the Enterprise is flung far away from the planet by an unknown force, and both the ship and the landing party find themselves--for lack of a better word--haunted by a mysterious woman. It feels almost like a ghost story in space, but without falling into any supernatural cliches. This is entirely a science fiction story, but one which doesn't get bogged down in techo-babble. It allows some mysteries to remain unexplained while explaining just enough at the end to make it seem plausible. Mood and atmosphere is a priority here, two cinematic virtues that defined season 3 but rarely get the attention it deserves (though admittedly other episodes did it even better).
I guess I can't fully articulate why exactly I think this is an underrated episode other than that it manages to be intriguingly different without feeling out of place from the rest of the series. It has less of a clear plot than f.ex. 'Spectre of the Gun'--another off-kilter and atmospheric episode from season 3 (and another favorite of mine)--but I'm completely hooked by this episode every time I watch it.