The episode opens with a scene on the "warship Voyager", quite obviously an unrealistic depiction of the ship which turns out to be the museum's recreation of events. Although the brutality and detachment of the crew is chilling, there are several dark, campy elements of the alternate reality that provide comic relief: the crew wear altered versions of their uniforms with no combadges or rank insignia, black gloves, and black turtlenecks. Chakotay's name is repeatedly mispronounced by the crew as ("CHAC-a-tay") and his tattoo has grown in size as to cover half of his face and appears in the design of MÄori TÄ moko markings. Janeway sports a butch haircut and excessive schadenfreude. Meanwhile, the Doctor has become an android mass murderer while Tuvok has adopted a sinister sense of humor; Seven of Nine is a full Borg with several other Borg drones serving as shock troops onboard Voyager. There are also numerous Kazon actively patrolling the ship with phaser rifles in hand, and Neelix is depicted as a bridge officer.
In the actual course of events, Captain Janeway had agreed to provide the Vaskans with medical supplies in exchange for dilithium crystals. The Kyrians, who were at war with the Vaskans, boarded Voyager to stop the deal, which they thought was a weapons deal of some sort. During their time on the ship, they stole a data module carrying a backup copy of the Doctor. 700 years later, this module was part of a Kyrian museum exhibit which showed their version of the encounter. This biased encounter showed Voyager as a warship with a savage and sadistic crew that was willing to commit genocide. Even the Vaskan in the simulation became horrified over the atrocities committed, but the simulated Janeway told him it was too late to stop now. A curator at the museum, always fascinated by Voyager's story even though they were "the bad guys", finally reactivated the Doctor. Initially, his claims that Voyager was depicted as unfairly malicious are ignored, and he is told he could be held accountable for war crimes. Eventually, after fending off an angry mob, he convinces the Kyrian curator to help him set the 700-year-old record straight. The episode ends an indeterminate number of years later, as the museum's new curator explains that the two species finally made peace thanks to the efforts of the Doctor, although he always regretted that he would never see any of his friends again. Following that, the Doctor served as the surgical chancellor for the Kyrians and Vaskans for many years, but eventually he took a ship and departed for Earth; he said that 'He had a longing for home'.