The season and the first two seasons come to their epic conclusion in "Basics, Part 1," and darned if that's not a tall order.
Having cut off most of what had been developing for the Seska-Kazon alliance earlier, our favorite Cardassian traitor instead unwittingly gets it back on track by stumbling into her own crisis, her bastard child finally being born, and she suddenly grows maternal and protective, contacting Chakotay, whom they both believe to be the father, asking for help, and of course he agrees, forcing Janeway (hey! this is the one time Chakotay really forces the action!) to enter a final confrontation with the Kazon, a situation that proves too chaotic for the ship to handle.
Seska uses the ensuing opportunity to once again align with the Kazon, who steal the ship and exile the crew to a desolate world, sort of putting everyone in the reverse of how the series pilot ended. It's quite a dramatic event, even if you were one of the fans who never cared for the Kazon. They were seen as the poor man's Klingons from the start, and many fans wanted to have seen the last of them after their first appearance, but they kept coming back, and eventually found a strong ally in Seska, and like it or not became a huge part of the series.
Now, many, many times hostile aliens have taken over the ship/station in Star Trek, sometimes so easily that it ends up seeming like a joke. I confess to having sometimes thought of "Basics" as one of the more forgettable instances of this trend, but it's incredibly important in how it galvanizes the crew in unexpected ways. For one thing, it forces the recurring Lon Suder into becoming a key character in the series in ways he's hadn't already been, and also places the Doctor into harm's way and forced to fend for himself for the first time (but that's really for the second part; it does, however, in its implication from this half of the story reveal him to be in a most unique position for Star Trek), and not to mention Tom Paris once again being the odd man out, something he routinely becomes, even after finally joining a lasting family, when he's left on his own to come up with a plan of rescue (more on that next season!).
Anyway, the stakes can seem a little silly when all you're talking about is a single ship and the only thing the good guys really lose is the ability to get home, but they still alive, right? That may be the whole point of the series, but there were still possibilities, right? Except you want those bad guys to finally get it, and there's no better opportunity for that to happen than when it seems like they've finally gotten everything they wanted. How often does that happen in Star Trek? Really, only during the Dominion War. That's the power of keeping a story going for a while. That's what benefits the series from keeping around unpopular villains, because they force one major character into action, and then everyone else into jeopardy, and finally everything into a place where they either move forward or truly get left behind.
Well, hey, that sounds like a winner to me.
franchise * series * essential * character
Anthony De Longis
Memory Alpha summary.