Having returned from a two-week away mission of scanning planets and gathering dilithium ore, Chakotay, Tom, Harry and Neelix begin experiencing strange visions. While Tom dreams he is engaged in an alien battle, Harry has an anxiety attack during a routine check of a plasma leak. Meanwhile, Chakotay suffers from violent dreams that put him in the middle of an offensive, and Neelix, reacting to the weapons fire he is hearing in his head, takes Naomi hostage in the mess hall.

Once the Doctor runs some tests, he discovers the increased engrammatic activity of Chakotay and the others suggests they are reacting to memories, not delusions. As Janeway asks them to retrace their mission, they begin having flashbacks of their roles in an attack force against the Nikon. Commander Saavedra ordered them to evacuate the Nikon from their remote colony, but a small group of the colonists began firing weapons. Chakotay and the others on the force panicked in the ensuing chaos and shot back, murdering 82 civilians in the process.

Trying to piece together the puzzle, Janeway orders Voyager into the system the away team was scanning and joins Seven in reviewing the Delta Flyer's sensor logs. As soon as the Captain sees Tarakis, the second planet encountered by the away team, she also begins having flashbacks of the massacre. She remembers pleading with Saavedra to admit their mistake, but he continues to vaporize the evidence of the colonists' bodies. When she wakes up later in sickbay, Janeway learns that other crewmembers have also begun experiencing the battle memories.