"Maneuvers" is the essential episode of the first two seasons of Voyager. And it stars Chakotay.
There are dozens of misconceptions about Voyager, one being that it made every mistake possible. The reverse couldn't be more true. In its first episode the series outlined everything that it was going to be, and very wisely the producers set about exploiting that first episode for two seasons, including a perennial foe the crew could butt heads with on a repeated basis, semi-savages aliens known as the Kazon whom fans mistakenly identified as unworthy of their attention.
How were they relevant? They provided an outlet for those members of the combined crew who didn't trust it, led by Seska, the Cardassian spy planted within Chakotay's Maquis cell who posed as a Bajoran and was quickly exposed in the first season and officially defected to the Kazon, who were splintered into the very factions Janeway had successfully eliminated in her own crew.
So "Maneuvers" is the episode where Seska and Chakotay finally have their reckoning. It's not the beginning or end of the arc that only really concludes in the third season premiere (with a wicked reverberation in the later "Worst Case Scenario"), but speaks to the power of everything that comes before and after it, not only the dramatic worth of the Kazon, but how significant a character Chakotay really was when written in that way.
For most of the series, he defers to the judgment of Captain Janeway, but on the rare occasions where he finds himself in control, he is a capable and confident individual, who nonetheless struggles to keep his emotions out of it (this instinct got him in trouble in his youth, and he's spent the rest of his life keeping it under control, like a human illustration of Vulcan history; no wonder he ends up with Seven, and it's assumed that anyone who actually paid attention would understand). He has no control when it comes to Seska. Hers was the betrayal he couldn't ignore.
And so "Maneuvers" happens. This is the epic story that lies in one significant corner of the whole series. And really, where else could Chakotay go after it?
franchise * series * essential * character
Anthony De Longis
Memory Alpha summary.