While I wouldn't say "Distant Orgin" was one of the darkest Star Trek episodes, it did have a rather sinister dark side to it. Odala, the matriarch of doctrine, was like the old style Roman Catholic church punishing Galileo for his beliefs. The first sign of a possible dark episode was finding the obvious Voyager crew member remains on a planet. It left some presumption that Voyager met its demise somewhere down the line. In some respects, it looked like the planet where the Voyager crew was marooned by the Kazon and some of the crew were killed by the lizard creature.
So these Voth aliens appear on Voyager observing the crew clinically as "specimens"... and it's unclear if they'll decide to abduct some of the crew. They ultimately do end up taking Chakotay.
Then there's the Voth mothership, demonstrating immensely superior technology. While we know that Voyager must continue, as the series has multiple seasons ahead (so the ship can't be destroyed), there is this point where it's uncertain if the ship might be permanently detained or destroyed. When Odala places judgement, we're suddenly seeing the whole crew of Voyager possibly doomed to live their lives on an alien prison colony. Finally, Odala strong arms her paleontology scientist to retract his claim, and thankfully Voyager is freed. That Odala matriarch was quite unnerving. Very powerful, and very arrogant.
The actress who played Odala was Concetta Tomei. I'd never seen her in other productions. I thought she was an absolutely perfect choice for that role, as she wore it very convincingly.
