Enterprise learns the fate of a human colony not heard from for 70 years. When the crew arrives, they discover unexplained radiation at the site of the colony. Understanding that radiation levels 70 years ago would have been lethal, however, they find people still there and living underground.
Enterprise is investigating Human's first deep-space colony — Terra Nova, nine years away from Earth at early warp speed. The colony had not been heard from in the last 70 years, following a disagreement with Earth regarding further colony ships. Captain Archer, Ensign Mayweather, Lieutenant Reed, and Sub-Commander T'Pol take a shuttlepod down to the surface, where they find a ghost town and radiation that would have been lethal seventy years earlier. Reed then detects a humanoid and gives chase, arriving at a cave entrance — inside Archer and Reed make first contact, but Reed is soon shot and captured.
Back on Enterprise, T'Pol reveals that the attackers were human, not alien. Archer notes 52 bio-signs in the cave network including Reed's. He decides to negotiate, and takes Doctor Phlox down to the surface. Two colonists, Jamin and Nadet, bring them to Reed, who is stable. Phlox also finds that Nadet, Jamin's mother, has lung cancer, and she is taken back to be cured. While being treated, T'Pol shows her records that the "poison rain" was caused by an asteroid strike and not by any treachery by Earth. Furthermore, the radiation stopped any distress calls from reaching Earth. Archer explains that Novans and Humans are actually the same species.
Archer and Phlox try to convince them to leave, since Phlox is unable to manufacture an antidote. 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 makes the connection, but Jamin reminds Archer that Reed will be killed if they are not returned soon. T'Pol argues that relocation to Earth would save their lives but destroy their Novan culture. Finally, 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 planet's unaffected southern hemisphere.