The Enterprise is sent to shed lights of a decade old mystery. Roughly, 75 years earlier, the spaceship Conestoga leaves the Earth to a nine-year journey to establish Terra Nova, the first human colony outside the solar system. This colony has thrived prompting the Earth Space Agency to send another vessel. The Terra Nova colonists protested until transmissions ceased all together.
Gathering again at the Captain's Mess Hall, Archer, T'Pol and Trip discuss their new mission. T'Pol informs them of her ignorance of the Terra Nova colony.
Archer tells her that it is Earth's Great Experiment into discovering whether humans could colonise a planet in deep space. Earth is able to build New Berlin on the Moon, Utopia Planitia in Mars and other colonies on asteroids. Terra Nova is to be the first colony outside the solar system.
Upon reaching Terra Nova, the Enterprise hails the colony but they are not able to get an answer. Scanning no bio-signs, the colony looks intact. T'Pol reports low-level radiation but is unsure of the source. Archer gives the bridge to Trip and takes a shuttle to the colony with Mayweather, Reed and T'Pol.
On the surface, the team is assured that there has been no attack to cause the colony to become a ghost town. Mayweather proceeds to the communications tower to try and secure transmission from Terra Nova.
T'Pol calculates that radiation levels 70 years ago would have been lethal and assumes this could have caused the colonists to evacuate. But Archer points out that the buildings are made from parts of the spaceship thus preventing departure.
Reed has detected humanoid life signs in the forest at the colony's edge. He is able to determine that it is two metres tall with scales on its face. They radio Mayweather to meet up with them.
T'Pol and Mayweather guard the entrance while Reed and Archer proceed inside. They discover signs of people living in the caverns. Looking up, Reed sees faces observing them from a ledge. Archer asks the figures if they know what has happened to the colonists; but Archer, seeing a humanoid form holding a gun, fires his phase pistol and stuns him. The faces on the ledge disappear. Then, shots are aimed at Archer and Reed.
They are able to escape but not before Reed is shot at and jumped by another humanoid. Forced to leave Reed, he returns with T'Pol and Mayweather to the Enterprise. T'Pol reveals that their attackers are human life forms and not aliens.
Scans on the Enterprise reveals the series of tunnels in the cave and 52 bio-signs including Reeds. A transport is out of the question as his location is too far in. A rescue attempt is formed but Archer decides to negotiate with the colonists so they could avoid an encounter.
Archer returns to the colony with Phlox while T'Pol tries to discover the source of the radiation and Mayweather and Hoshi work on the data buffer from the communications tower.
Archer and Phlox walk together in the forest as they want to be caught so they could be face to face with the colonists. They find Reed in good condition. Archer talks with Jamin and Nadet, old colonists who are able to converse in English.
Archer is informed that they are called Novans and asks if the Enterprise is there to kill them. They believe that the humans have sent poison rain that injured many Novans. Archer informs them otherwise, and offers to work with them to discover what has really happened. Archer further convinces them to let Phlox treat Reed. While Phlox is treating Reed, he scans Nadet and informs them that she has lung cancer. She can be cured but she has to go on board the Enterprise. Jamin agrees but asks that Reed stay behind for security.
On board the Enterprise, they are taken to Sickbay where Phlox determines the extent of Nadet's cancer. She is given cytolitic injections. While they wait, Archer informs them of T'Pol's findings. T'Pol has discovered an impact crater where an asteroid has stricken 70 years ago. The asteroid is made of barisium ore and the impact has created a cloud that would have been radioactive and dangerous to the colonists. From the data buffers, Archer is able to determine that the Novans believe they are being attacked. The adults die out and the children live on believing that humans are their enemies.
To avoid the extermination of the Novans, Jamin and Nadet are convinced to relocate to the southern hemisphere where there are no effects of the radiation.