Professor Gegen and his assistant Veer find the remains of a Starfleet officer in a cave on an alien world. Gegen feels the evidence holds the key to the real origins of his race, the Voth, a saurian species that he suspects got its start in a distant part of the galaxy. The "Distant Origin" theory contradicts the doctrine of Chief Minister Odala and the powerful Voth elders, who believe the Voth were the first intelligent beings to evolve in the quadrant. The elders are unreceptive to his claims, but Gegen finds a clue on the deceased's uniform: the name of a ship called "Voyager."
Gegen and Veer trace Voyager's path across the Delta Quadrant and finally find the ship itself. Thanks to their sophisticated cloaking technology, the Voth are able to transport onto the ship and observe the crew undetected. Eventually, Voyager's sensors detect the use of cloaking technology on board the ship, and the crew uncloaks Gegen and Veer. Frightened, Veer fires a tranquilizer dart at Chakotay, but is himself incapacitated by a phaser blast. Gegen transports back to his vessel with the unconscious Chakotay.
In Sickbay, Veer goes into protective hibernation. The Doctor discovers that Veer has evolved from Earth's dinosaurs. On the Voth ship, after Chakotay regains consciousness, he and Gegen come to similar conclusions, reasoning that the Voth's ancestors survived extinction, developed space-faring technology and left Earth. Charged with heresy by the Voth elders, Chakotay is the best proof of Gegen's theories. But before he can take Chakotay to his supporters, the U.S.S. Voyager is transported inside a massive Voth city-ship.
The crew is held captive by the Ministry of Elders, who vow to kill them all unless Gegen returns to face them. Gegen agrees to confront his accusers and Chakotay promises to help him. Since their fate is tied to Gegen's, the Voyager crew eagerly awaits the results of his hearing. Odala accuses Gegen of being a destructive influence on Voth society and orders him to disavow his claims. But Gegen refuses to back down until Odala threatens to send the crew to a detention colony. To save them, Gegen retracts his theory, resigning himself to the fact that the Voth's true heritage will remain a secret — for now.