Professor Gegen and his assistant, Veer, two Voth palaeontologists, make a shocking find on a nearby planet: the skeletal remains of a creature whose genome is so closely related to their own that it could only have evolved on the same planet as the Voth did.
It is an individual from a technologically advanced species, judging by its synthetic clothing, a gold and black Starfleet uniform with a Maquis insignia. (The specific human is Crewman Hogan, killed in the earlier episode "Basics.") The scientists analyze the bones in their lab. The creature was an endotherm, probably a mammal, unlike the reptilian Voth. Still, the genetic similarities intrigue the scientists and they make a dangerous hypothesis, one which will need strong scientific evidence to convince the dogmatic elders of Voth society that their theological explanation for the origin of their species is not total truth. The archaeologists surmise that the creature in their lab evolved on a distant planet, and that the Voth evolved on the very same planet. This is the basis of the "Distant Origin Theory", one which is not accepted in Voth society because it contradicts doctrine that states that the Voth are the "first" race, which evolved in the area of space they now occupy and have ruled it for many millions of years.
A few Voth scientists are closet believers in Distant Origin and have worked to present evidence that might support their ideas. These scientists are considered subversive by many, but Professor Gegen is determined to prove Distant Origin, risking his career to bring his society out of ignorance and belief in myth.
Further analysis of the creature's garments and information from traders and merchants bring the archaeologists closer to finding the crewmates of the endotherm. They seek his ship, Voyager, and its crew, which call themselves "humans". Once they track down the ship, Gegen and Veer shield themselves and venture on board to observe their distant relatives. The humans are certainly mammalian, complete with a strange odor and a lack of scales. The scientists observe an intriguing courtship ritual between a male (Paris), and a female (Torres). The society of the humans is apparently rigidly hierarchical, perhaps a matriarchy as evidenced by the dominance of one female (Janeway).
The ship's sensors detect some sort of cloaked intruder on board. The crew goes on alert and seeks out the invisible infiltrators. Chakotay's phaser set to the right frequency brings the Voth into phase, and in a panic, Veer shoots him with a poison dart. Tuvok stuns Veer, and Gegen grabs the tranquilized Chakotay and transports back to his ship with him, where he plans to study the live human. In Sickbay, The Doctor does the same with his patient, who has just put himself into a state of hibernation. The Doctor discovers the genetic similarity. By running models on the holodeck he and Captain Janeway discover that the Voth are descendents of hadrosaurs, probably of genus Parasaurolophus.
There is no time for more research, however, when Voyager is accosted and beamed into the belly of a massive city-ship and shut down. It's the Voth, who plan to destroy the humans as threats to doctrine.
The Voth elders take Gegen into custody and put him on trial for heresy. Even though he brings Chakotay with him into the courtroom as evidence of the genetic link between Voth and human, the head elder, Minister Odala, presents findings from obviously doctrine-loyal scientists that explain the similarities as random convergence. She then introduces the star witness against Gegen, his assistant Veer. The younger Voth has been coerced into recanting his claims supporting Distant Origin. Odala gives Gegen a chance to recant his as well.
Odala is disgusted by Gegen's assertions regarding the truthfulness of Distant Origin. She notes that the Voth have been spacegoing for so many millions of years and have dominated their area of space since ancient times; they couldn't possibly be refugee "immigrants" from a faraway planet crawling with mammals. Chakotay points out that the doctrine of the Voth has been changed many times to conveniently explain truth via myth. The minister dismisses this and gives Gegen one final chance. He refuses to retract his theories and Odala convicts him of heresy and remands him to a prison colony. She then condemns the crew of Voyager to the same fate.
To prevent the imprisonment of the humans, Gegen retracts the science he believes so strongly in, and states that he is wrong. Defeated and hopeless, he agrees to take a position in another area of research. Minister Odala releases Chakotay and demands the humans leave Voth space forever. But as Chakotay and Gegen are saying good bye to each other, Chakotay presents him with a globe of the Earth. Gegen tells him that one day, all Voth will realize that the Earth is their home.