Museum spectators of a curious alien race an indeterminate number of years after their dealings with the Voyager Crew and their conflict with another race watch record of their history during the time the Doctor's program was brought 700 years into the future after the dealings with their people. They watch as how the doctor sets the record straight and ended conflicts between the two races. The real spectators were not revealed until the very end of the episode where it shows them watching record and explaining the events of their history
The episode opens with a scene on the "warship Voyager", 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, but sport black gloves and turtlenecks. First Officer Chakotay's name is repeatedly mispronounced by the crew and his tattoo has grown in size as to cover half of his face and appears in the design of MāoriTā moko markings. Captain Janeway sports a butch haircut and excessive schadenfreude. Meanwhile, the holographic Doctor has become an androidmass murderer while Tactical Officer Tuvok has adopted a sinister sense of humor; former drone Seven of Nine is a full Borg with several other Borg drones serving as shock troops onboard Voyager - this is possibly an insight into what would happen later on in Voyager when the Borg children arrive on board. There are also numerous Kazon actively patrolling the ship with phaser rifles in hand, and Morale & Mess Officer 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 military alliance of some sort. During their time on the ship, they stole a data module carrying a backup copy of the Doctor. Seven hundred 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. Quarren, the curator at the museum, always fascinated by Voyager's story even though they were "the bad guys," had found (with the help from an archaeological team) the Doctor's backup module three weeks prior. He was able to activate it using Voyager's own tools. The Doctor, upon seeing this biased simulated version of history is appalled and offers to show Quarren his own accurate version of events from 700 years ago aboard Voyager. Initially, the Doctor's claims that Voyager was unfairly depicted by the Kyrians are ignored, and he is told he could be held accountable for war crimes when he presents his version of history before the Commission of Arbiters. The Doctor states, however, that a presently non-functional Starfleet medical tricorder would settle the issue of who killed Tedran, a Kyrian revolutionary hero who died during a raid on Voyager if he can only locate and repair it.
After fending off an angry mob determined to destroy the tricorder—and the evidence that it contains—the Doctor initially wishes to abandon his quest to set the 700-year-old historical record straight and says that the truth may cause more harm and violence but Quarren, objects saying that the tension between the Kyrian and Vaskan world's has already reached the breaking point. Quarren stresses that both peoples on his planet need to hear the truth about the real course of events on Voyager and this persuades the Doctor to continue searching for the tricorder. 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 and the information from the tricorder, although he always regretted that he would never see any of his friends again. It is revealed to the viewer that all the scenes that we had been witnessing was a computer simulation revealing real life events which occurred in the past such as the Kyrian-Vaskan conflict, Quarren's discovery of the doctor's backup program, and Quarren and the Doctor's proposal to the Commission of Arbiters. Following the peace, 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." As for Quarren, it is stated that he lived only 6 years after seeing the Kyrian-Vaskan reconciliation.
Jamahl Episcophan of Jammers Reviews writes that Living Witness:
"is a standout story that is well told and thoroughly engaging. It features a central problem that is both relevant and unique. I haven't seen a Voyager outing quite like this one, and it pleases me to take in a story that can get its hooks into us for an hour and make us care about what's happening on the screen...."Living Witness" isn't quite perfect, but it manages to pull off a balancing act of Voyager-esque elements and come off wonderfully. It's original and entertaining, and it made me care about the characters, the most important of whom weren't even Voyager crew members."