"Threshold" is that episode that proves that even Star Trek fans can be bigots.
There's no other way to put it. It's the one where Paris and Janeway cross the warp barrier and eventually turn into lizards. Apparently this was horribly offensive, especially because most sci-fi (including, famously, the final episode of Babylon 5) likes to believe that the only way to go is a being of unlimited ability. Q suggested that this was the fate of humanity in "All Good Things," and the franchise littered the stars with beings of exactly that description. Of course, it also went out of its way many times to explain that "absolute power corrupts absolutely" (as Riker explains when he gets himself a taste of it).
So who's to say where evolution really leads? Isn't it a little bit vain to say that we know?
It's hubris and ego, then, that've defined the reaction to "Threshold" for almost twenty years, and it's about time to turn that around. This is a great episode. For one thing, it's far more about Tom Paris than evolution and lizards. It's about him worrying about his legacy, one of the few characters at any moment in the series to express concern that what he does halfway across the universe can still somehow matter to people he may never see again. He's trying to get everyone home, sure, but he's also trying to make history. He's desperate. In any other Star Trek series, this would have been the actions of the guest star. In Voyager, it was a main character.
It's a defining episode for Paris, and that's something that's been obscured by fans reacting against something they can't possibly understand, and besides, it's science fiction. If a little errant speculation isn't possible, then what's the point? Seldom does Star Trek even bother to do this sort of thing. If anything, "Threshold" should be a milestone, not a cautionary tale. In fact, that's exactly what it was supposed to be, but for Paris, not the series. Funny how things can sometimes turn out.
Far from one of the worst episodes ever, it's one of the best. And it's high time people know that.
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Memory Alpha summary.