Professor Gegen and his assistant Veer, two paleontologists of a space-faring saurian species known as the Voth, discover the skeletal remains of a human member of Voyager's crew, though they are unaware of its origins. Instead, they are fascinated by the similarity of its genome to their own species, and Gegen suggests that this supports the highly controversial Distant Origin theory, that the Voth had originated on a far-distant planet instead of the current area of space from which they rule their empire. Proof of the Distant Origin theory has been sought by other Voth scientists, but the heretical theory has often led to their exile.
To confirm their proof, Gegen and Veer track down the origin of the skeleton, learning of Voyager's presence in the Delta Quadrant. They locate the ship and transport aboard while cloaked, observing the mostly human crew in the setting. Voyager's sensors detect their presence, and the crew reveals the two Voth. Veer responds instinctively by releasing sedative-tipped needles that strike Chakotay; Geger grabs the human and transports him aboard his ship, fleeing from Voyager. The Doctor examines Veer and identifies the similar genetic structure; he and Captain Janeway use simulations to determine that the Voths descended from the hadrosaurs, probably of genus Parasaurolophus.
Gegen wakes Chakotay, and explains the situation, requesting Chakotay accompany him when he presents his evidence to the Voth elders; meanwhile, Voyager is captured by the Voth. Gegen is put on trial for heresy, and it soon becomes clear that he has been pre-judged guilty and the "trial" is only an opportunity for him to recant and reduce his punishment. Veer, recovered from Voyager, is coerced to act as a witness against Gegen by Minister Odala. Chakotay attempts to argue for Gegen, noting that the Voth theory of origins has changed so much to fit what the Voth wish to believe and not reality. Odala rejects this, sentencing Gegan to a prison colony unless he recants. When he still refuses, she then orders Voyager destroyed and its entire crew, the evidence for his theory, also sent to the prison colony. Gegen, unwilling to see them destroyed, realizes he has no choice but to recant.
Odala assigns Gegen a new job, and orders Voyager to leave Voth space forever. Before departing, Chakotay gives Gegen a globe of the Earth, which Gegen acknowledges that someday, the Voth will accept as their home world.
The story is told largely from an alien's (Gegen's) perspective, with the Voyager crew having very little activity in advancing the plot. It is also a rare case of a Star Trek episode exhibiting one of Arthur C. Clarke's ideas that sufficiently advanced technology is indistinguishable from magic. Voyager's systems and weapons are rendered useless by the Voth technology, and the crew is left helpless while their fate is decided.