|You know it makes sense|
The episode "Threshold" (VOY) is often regarded as one of the worst, or the worst, in Voyager, or indeed Star Trek. But, while it's pretty hard to argue it's a great episode, it is both interesting and significant. Even if daft.
Tom and Transwarp
Tom Paris and Kim devise a new "transwarp" drive which will reach warp 10. Star Trek's use of "warp factor" speed varied over time, which can be explained as recalibration. At the time of Voyager, warp 10 would be infinite speed, so that high speeds represented between 9 and 10. Warp 10 is believed impossible by their theory. You would be everywhere at once.
However, Tom Paris and Kim develop a "transwarp" drive that can reach warp 10. If it works, Voyager could get home and the world would be transformed. Tom makes the first flight, but soon after his return his body starts to degenerate. The Doctor can't save him and he dies. But then a bit later he revives, and starts changing into something non-human. It's pretty weird, and in fact the episode got an Emmy for make-up. Apparently he is undergoing, in a matter of hours, the future direction of human evolution. He becomes irrational. The Doctor finds a method of restoring him, but before it can be implmented Tom escapes, kidnapping Captain Janeway, and zooms off at transwarp.
A few days later Voyager manages to find them. They are on an uninhabited planet, where they have become a couple of giant amphibians looking rather like salamanders. What's more, they have mated and produced some youngsters, which (who?) slip away into the water. The crew bring the Janeway and Paris salamanders back, and the Doctor successfully restores them, by means of anti-protons.
Firstly, let's get one thing out of the way. The plot is as full of holes as Swiss cheese, but this isn't Agatha Christie. A perfect plot with every end tied up is not the point: lots of Star Trek has plots that don't add up. It's true that in this case, the faults are rather noticeable, but no more than in some other episodes.
The most significant part of the episode, and one that generally gets overlooked because of the weirdness of the rest, is a character story about Tom. When they are preparing for the transwarp flight, Captain Jameway is going to have Kim replace him as pilot as he has some unusual medical risk. It's small but she thinks it's an unnecessary risk. Tom pleads to be allowed to go. When he was growing up, there were expectations that he would be something special, achieve something special. Instead of which he disgraced himself. This is his chance to do something. As Captain Janeway had remarked earlier, he would be one of a short list: "Orville Wright, Neil Armstrong, Zefram Cochrane and Tom Paris". He may be risking his life, but "this is the first time in ten years I feel I have a life to risk." There is a degree of emotional desperation that Tom doesn't usually let show. The Captain agrees to lets him make the flight.
When Tom is dying, he starts rambling, recalling that his father thought crying was a sign of weakness, but that he disagreed. "What I remember most about being a kid are the times I spent in my room crying. I liked my room, though. It was quiet in there. People would leave me alone. I'd keep the door locked, read, play games. I lost my virginity in that room. Seventeen. Parents were away for the weekend." (The Doctor comments "I'll note that in your medical file.") His last words are about how they must tell his father about the transwarp flight.
When he revives, he is rambling in a different way. Previously the sadness of his emotional background was coming out; now it's the anger and frustration. "You're lying. Just like him. Just like everyone around here. Always lying. Always telling me that I'm doing a good job, that you're glad I'm on this ship. But none of that's true. Why can't you just say it? You're jealous that I broke the transwarp barrier, and now you're hoping I'll die!"
At the end, when restored, Tom reflects that he had thought being a hero would make people respect him and solve his problems, but perhaps the opinions he needs to change are his own.
All of this, despite the bizarre setting, is an important step in Tom's development as a character—and Tom's development is one of the most important stories of Voyager. 
What about the transwarp flight itself? The interesting suggestion has been made (Rachel Carrington, "Threshold and the Overlooked Message of Reaching for Success") that there is a message for us: the fact that an achievement was followed by unexpected problems doesn't mean that it wasn't an achievement, and it is better to try things than to stand back and do never do anything, because of risks. Captain Janeway recommends Paris for a commendation because, despite what happened, he did achieve transwarp.
Evolution and Salamander Sex
OK, now we come to the bit about evolving into salamanders.
It has been objected that the idea of a future course of evolution which can somehow be foretold is a serious misunderstanding of evolution. But "Threshold" is not alone or even unusual in Star Trek in this. There are several cases where some change is supposedly "the next step in evolution" (commonly the acquisistion of paranormal powers). In fact, "Threshold" makes more attempt to make sense of it than most. The Doctor comments that the changes seem to be a continuation of a direction followed for the past few million years, and suggests that the warp 10 experience, transcending time, may somehow have linked Tom to future human descendants.
But it's not the logic. Lots of Star Trek is illogical. It's the salamanders.
Tom is supposedly evolving into a later, and probably more advanced sort of human being. But the salamanders seem to be rather less than human. Their offspring are left behind; the crew seem to feel that they aren't a sort of human they could bring alone, just some rather bright salamanders. (I wonder how the Prime Directive applies here?) So does the future state of humanity go downhill again? The idea is curiously reminiscent of the early science fiction story "The Man Who Evolved" by Edmond Hamilton (1931). A scientist invents a machine which can advance him in future human evolution, in fifty million year steps. Observed by his friends, he becomes progressively more and more intelligent and cerebral, until the last step turns him into primitive protoplasm—apparently evolution is circular. 
At the end, Captain Janeway and Tom Paris are sitting a bit uncomfortably in sickbay. Tom starts to apologize, saying that although he doesn't remember much... but the Captain cuts in "What makes you think it was your idea? Sometimes it's the female of the species that initiates mating." For your morbid interest, amphibians mate both by internal and external fertilization. It's important to get these details clear. They also sometimes reproduce by parthenogenesis, so it is not actually certain that they did do the (salamander) deed.
But the ultimate argument in favour of the salamanders is that the episode is interesting to watch, and even to re-watch. There are many far "better" episodes that are forgettable and far less engaging.
 I asked ChatGPT to produce an argument that it was a great episode, comparable to the classics, and it refused saying the task was too difficult. [Return]
 It makes sense that as ships get faster this would become inconvenient. In "All Good Things" (TNG) we see a future in which warp factors in the teens are mentioned. Perhaps infinite speed is now 20, or something. [Return]
 The dramatic purpose of this is rather unclear. It does allow one good scene where Tom asks Kes to kiss him, but she can't due to the odd atmosphere he requires at that point, and she then kisses him softly after he dies. (This seems to be the point of the special atmosphere, actually, since Tom doesn't need it when he revives.) But otherwise the break is very brief and we don't see any of the rest of the crew—no reactions from the Captain or Kim for example. [Return]
 Referring to it as an "Emmy-award-winning episode" may get some odd looks though. [Return]
 We're explicitly told later that Tom's metamorhasis is unrelated to this medical abnormality. [Return]
 Robert Duncan McNeill and Garrett Wang noted this in a 2020 discussion, "Kate Mulgrew, Robert McNeill, And Garrett Wang Revisit "Threshold," That Infamous 'Star Trek: Voyager' Episode". McNeill here gets a opportunity to expand his acting; though perhaps he would have preferred the opportunity to be in a different episode. [Return]
 Isaac Asimov (ed), Before the Golden Age, vol. 1 (London: Futura, 1975), pp. 37–54. The narrator wonders if the apparent ascent of evolution is in fact an illusion, doomed to a futile circle, or whether perhaps there is some higher change he cannot perceive. Like many of the stories in this collection, the story is technically unsophisticated but wonderfully imaginative and memorable. [Return]