The U.S.S. Voyager and its crew are on display in a Kyrian museum 700 years in the future, and they are being blamed for a horrible civil war that nearly wiped out the Kyrian race. Through inaccurate simulations, the crew is shown as violent people who did not hesitate to destroy anything or anyone standing in their way of getting home. Approached by the Vaskan Ambassador for help in his fight against the Kyrian, Janeway supposedly slaughtered millions of innocent people in exchange for wormhole travel to the Alpha Quadrant.
The museum curator, Quarren, works within the engineering simulation to access a data storage device recently uncovered at one of the Kyrian ruins. When he realizes it is a hologram, he activates the Doctor's program and explains what has happened. The Doctor is distraught and refuses to believe that 700 years have passed, but he soon sees the Voyager artifacts in the museum and knows it must be true.
Appalled by the depiction of Janeway and the crew as cold, heartless thugs, the Doctor tries desperately to describe Voyager's side of the story. Although he explains that Janeway had just negotiated a trade agreement with the Vaskan Ambassador when they were attacked by the Kyrian, Quarren balks at the idea that his people were the aggressors. When the Doctor describes how Janeway and the crew only wanted to extricate themselves from the war, his program is silenced.
After some time to think about what the Doctor has said, Quarren allows him to create a simulation of his own. It shows that the Kyrian leader, Tedran, invaded Voyager. Janeway explained that they were trading with the Vaskans and nothing more, but Tedran wouldn't stand down. It was the Vaskan Ambassador who killed him, and the last thing the Doctor remembers is Kyrian ships attacking Voyager. As he works to reactivate his medical tricorder and offer proof of his re-creation, a group of angered Vaskans breaks into the museum and begins destroying it.
When war between the two groups threatens to erupt again, the Doctor believes it would be best if his program is decompiled. Although he wanted to clear Voyager's name in history, it's not worth causing more fighting. Years into the future, watching another simulation, people see Quarren talk the Doctor into giving his testimony of events. Because of that, the great war was finally portrayed accurately, and harmony was restored. After setting the record straight, the Doctor eventually boarded a shuttle for the Alpha Quadrant to trace Voyager's path home.