Remember Kes? Well, this is the episode that makes the crew wish they didn't, and vice-versa, because she makes her first (and final appearance) since her departure at the start of the fourth season, when everyone thought she was going on a lovely and magical journey of self-discovery.
Having a former series regular come back is rare enough in the franchise, it's got to be considered fascinating every time it happens. Fans at the time were horrified to see Kes turn into such a spiteful creature, but with the only other precedent for this being Tasha Yar, it was bound to be a risky move for the series.
But really, it not only makes sense, how "Fury" handles the situation, it makes all the sense in the world. Maybe after two seasons it was easy to forget just how unstable and fragile Kes really was (though there were certainly long stretches where she seemed to be the most rational person in the room). It might be easy to forget that her journey was into uncharted territory, and that she rarely demonstrated the ability to explore it without significant difficulties and guidance from, say Tuvok. In fact, considering how she regularly caused distress in others (Neelix, The Doctor, Tom Paris), should it really be a surprise that she would do it again?
"Fury" is that rare moment when Star Trek acknowledges that not everything ends up perfect after the end of an episode. Deep Space Nine was a seven-season example of this, but for most of the franchise, it was easier to believe that our intrepid crews did in fact solve all the problems they came across; when it seemed like a happy ending, then it probably was. Kes proved in very dramatic fashion that this wasn't even necessarily true of characters we'd known for years. (Just imagine what actually happened to Sisko's crew; even Worf didn't stick around as a mere Klingon ambassador for longer than it took for another reunion with Picard; but then, Pocket Books has done a lot of exploring how that worked out.)
Yes, Star Trek is the hopeful message Gene Roddenberry always envisioned, but even in the original series, not all reunions were happy (hello, Christopher Pike!). Consider "Fury" the biggest challenge Voyager ever gave to the franchise mandate.
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Memory Alpha summary.