The sixth season of the series was not exactly its most beloved. Okay, so it's the least popular season. Okay, so in some circles it was pretty much despised. Perhaps some of that necessarily stems from the way it opened. "Equinox, Part 2" concludes the story of Janeway's ideological clash with Captain Ransom, another Starfleet officer trying to make the long journey home to the Alpha Quadrant. Ransom seems to have made pretty much all the opposite decisions Janeway did, except for that one similarity, and this irks her in a moral sense.
The problem is, she ends up in a moral quandary once it becomes clear to her that she cannot sit by and let him continue. Like other Star Trek captains before and after her, Janeway develops an intense need to bring this nemesis to justice, but she seems to push it too far, threatening torture and execution in order to reach her goal. Even Chakotay is abhorred by this behavior, and usually there isn't a more dependable voice of agreement in her crew.
So the challenge is to watch this episode and judge for yourself, with or without a greater awareness of how Janeway has conducted herself. This makes it a key episode for the series and for Janeway herself, no matter your conclusions. (It may or may not be worth noting that the loose arc for the character during the rest of the season is one of redemption.)
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Memory Alpha summary.