Chakotay's shuttle has been shot down, and he is alone on a jungle planet. He is captured by the human-seeming Vori, lead by Brone (Michael Mahonen), but they (appear to) release him when they determine he is not of the "nemesis." Chakotay tries to find his shuttle the next day, and encounters one of these people known to the Vori as the "nemesis." They are called the Kradin and are fierce and non-human in appearance. Chakotay's shuttle is gone so he returns to the Vori. He bonds with them and immediately understands what they are up against. As he joins the Vori in the struggle against the Kradin, he sees evidence of the evil of the nemesis: they mock the Vori's religious rituals and send a peaceful Vori village to death camps.
Meanwhile, Voyager is orbiting the planet, unable to locate Chakotay. They contact the Kradin, who are amicable and agree to lend a jungle warrior team to retrieve Voyager's first officer. The Kradin explain that they are battling a relentless force called the Vori, whom they also refer to as "nemesis." Tuvok goes down to the planet and rescues Chakotay, who has actually been experiencing an elaborate training and brainwashing program to turn him into a Vori foot soldier. He has been thoroughly indoctrinated to believe the Kradin are monsters, and is disgusted by the sight of them. Once he is back on Voyager, he is presented with evidence that the Kradin are not the hate-ridden entities he thought them to be and that it was in fact the Kradin who helped locate the commander and bring him to Voyager. As they depart the planet, the Kradin ambassador makes an appearance in sickbay where Chakotay is recuperating. Due to his recent experiences in the Vori simulation, an uncomfortable Chakotay leaves sickbay and privately confers with Captain Janeway about the difficulties in putting aside his hatred for the Kradin.