The Enterprise learns the fate of a human colony not heard from for 70 years. When the crew of the Enterprise arrives, they discover unexplained radiation at the site of the colony. The radiation levels 70 years ago would have been lethal. However, they find people still there and living underground.
The Enterprise is investigating what happened to humankind's first deep-space colony - Terra Nova (Latin for New Earth), nine years away from Earth by early warp transport. The colony had not been heard from in the last 70 years, following a disagreement with Earth regarding further colony ships. Archer, Mayweather, Reed, and T'Pol take a shuttlepod down to the surface, where they find a ghost town and background radiation that would have been lethal seventy years earlier.
Reed detects a humanoid and gives chase, arriving at a cave entrance. The away team meet at the cave with flashlights, allowing Archer and Reed to investigate while the other two guard the opening. After an altercation, Reed is captured, and the other three return reluctantly to the ship. T'Pol reveals that the attackers were human, not alien. Archer discovers that there are fifty-two bio-signs in the cave network including Reed's. He decides to negotiate with the colonists, and takes Phlox down to the surface. Two colonists, Jamin and Nadet, bring the pair to Reed, who is healthy, though he's lost some blood. Phlox also finds that Nadet, Jamin's mother, has lung cancer, and she is taken back to the Enterprise to be cured, while Reed remains.
While Nadet is being treated, T'Pol shows her records that the "poison rain" was caused by an asteroid strike and not by any treachery by Earth. Archer explains that, while it may be difficult to believe, the Novans and Humans are the same people. Furthermore, the radiation stopped any distress calls from reaching Earth. Phlox discovers that Nadet and Jamin have signs of micro-cellular decay in their endocrine systems, probably from a polluted water supply. Phlox cannot treat it, and it will only get worse.
Archer and Phlox try to convince Jamin and Nadet to leave the planet. Archer shows Nadet a photograph of a family group outside a dome. She identifies them as human and says the photo was taken before the poison rain. Nadet looks confused, as she perceives humans to be enemies of Novans. Archer zooms in on a young girl sitting next to her mother - her name was Vera Fuller and the daughter was called Bernadette. Nadet makes the connection, but Jamin reminds Archer that Reed will be killed if they are not returned. Archer and T'Pol debate whether to relocate the people to Earth. T'Pol argues that relocation would save their lives but destroy their Novan culture. Finally, while on the planet, Archer gains the Novans' trust by rescuing one of them from a well, and persuades the remaining colonists to relocate to similar caverns on the southern hemisphere, which had not been affected by the radiation.