During a survey mission, Chakotay comes under fire and makes an emergency beam-out from his shuttle. He arrives on a planet whose inhabitants are locked in war, and is taken in by the Vori, a humanoid group that is fighting against the vicious Kradin. While searching for the remains of his vessel, Chakotay and a young Vori soldier battle two Kradin, and the Vori is killed.
After rejoining the Vori soldiers, Chakotay and the others set out to meet a larger group of soldiers, but on the way, learn their fellow Vori contingent has been massacred. Suddenly, the Kradin are upon them, and several soldiers are killed in the barrage of gunfire. Chakotay is wounded, but he gets away, fleeing into the night. At last, he comes upon a settlement of Vori and collapses.
Back on Voyager, the crew learns pieces of Chakotay's shuttle were found in the middle of a war zone. They are unable to contact him, but are promised by one of the planet's ambassadors that their friend will be located and returned. When Chakotay revives in the settlement, the residents tell him he can find communications equipment at the "Re-Stock Unit," which is some distance away. The next morning, he sets out to find it, but the sight of enemy aircraft brings him back. He returns to find the Kradin taking the people by force. Learning that the Vori elders will be exterminated, Chakotay tries to fight the enemy, but is outnumbered. Meanwhile, Janeway meets with the Kradin ambassador, who sends down a commando unit to accompany Tuvok in searching for Chakotay.
Left to die by the Kradin, Chakotay is grateful when a Vori leader comes back to free him. The two join in battle against the Kradin but Chakotay is shocked when one of the enemy calls him by name. Although he looks like a Kradin to Chakotay, the alien assures him that he is actually Tuvok! Tuvok explains that the Vori have been using mind-control techniques to get Chakotay to help fight their war. His encounters with the soldiers and the civilians in the settlement were Vori simulations training him to hate the Kradin. Although faced with the probability that the Vori are no better than the Kradin, Chakotay realizes that it will be harder to stop hating than it was to start.