The Kazon arc of the season has one of its essential elements play out this episode, in a number of intriguing ways.
For several episodes, we've known that Jonas has been conversing with the Kazon, feeding them information. He's a traitor, and he plays into Seska's hands. But he doesn't get away with it scott free. Tom Paris makes a big show of becoming disgruntled and actually leaves the ship this episode, another minor recurring arc coming to fruition this episode. Anyone watching the series from the beginning might assume that he's finally falling back on the character traits that defined him in "Caretaker."
Then we have Neelix of all people trying to figure out how the Tom Paris he's come to know has reached this point, and in the process uncovering Jonas' treachery. The whole affair is like a status marker. Some fans were still complaining (and still do) that the Maquis as a storytelling device were a lost opportunity, and yet they gave us Seska, Jonas, and Suder, all characters who would never have existed in any other Starfleet crew, doing things no other Starfleet officer would have ever done, and each of them brought their drama into the second season of the series, and forced the rest of the crew to reveal their greatest strengths. Earlier in the season Chakotay benefited from it, and now in "Investigations" Paris and Neelix do.
Paris struggled hard to prove he wasn't just the callow outcast he first appeared to be, just as Neelix tried and continued to try well after this that his outsider status had unexpected benefits. Neelix was never going to be a character who exposed the human condition like Spock or Data, because he was, for the most part, extremely happy to be himself. But every now and again, he saw something just differently enough to question things that needed to be questioned, and caught the crew in their complacency. That's how he figured out what was really going on. That's why he made such a good match for Tuvok. Because they really weren't so different.
"Investigations" is one of the most important episodes of the season, and yet it's long stood as one of the most forgotten. Hopefully that's something that can change, too.
franchise * series * essential * character
Memory Alpha summary.