This episode of Enterprise written by Rick Berman & Brannon Braga, sees the crew on its way to Terra Nova, a colony that just up and vanished one day. It is a sci-fi version of Roanoke, the colony in North America that vanished with nothing but a word written into a tree.
No one knows what happened here, it seems that relations between Earth and Terra Nova became difficult. They didn't want another colony to set up on their world. One day they just stopped responding to Earth. It has been 70 years since anyone has heard from them. T'Pol asks why Earth didn't ask the Vulcans to reach out to them and Trip simples replies that asking Vulcans for help comes with too much baggage.
The Enterprise finds the colony, it is intact but there seems to be no one around. However there is radiation on the surface. Not a lot but enough that staying for a long time could cause problems. Archer, T'pol go down to the surface with Reed and Mayweather to see if they can find any clues. It seems the radiation 70 years ago, when they stopped talking to Earth would have been deadly. But if that killed them then where are the bodies? T'Pol asks if they could have left but it seems their city is built out of the ship. Reed finds someone running in the woods and gives chase.
The person leads them down into the caves where Archer and Reed follow suit. T'Pol and Mayweather stay topside to keep look out. Archer ad Reed find weird looking aliens. He tries to talk to them and as if they have seen any of the people from the surface. A fight breaks out and the captain and Reed take off running. They call T'Pol for directions on how to escape from the tunnels. Reed gets shot but it isn't bad, he starts forward but is captured by the aliens. They keep firing preventing Archer from going back for them. One of the aliens attack Mayweather but T'Pol saves him. The three of them take off leaving Reed behind. T'Pol tells them that her scans show they aren't aliens, they are in fact human. There are over 50 of them in the underground caves.
Archer and Phlox go back to the surface to try and find Reed. The humans take them down to the tunnels to find them. They seem to deeply distrust humans. They don't think that they are humans. They want Archer and co gone. Arche agrees they just need to get Reed up and running again. The people on this world think that the humans dropped poison on them and drove them underground. Only one person there, an older lady is the only one who was alive 70 years ago when it happened. She was nothing more than a child when it happened. Archer tries to tell them that they too are human and they don't want to believe Archer.
It seems the old lady has lung cancer and needs treatment. Phlox offers to treat her but she needs to go back to the ship. Her son demands to go with her and that Reed stays here to assure that no harm comes to them. Reed agrees and Archer goes along with it.
Archer keeps trying to convince them that they use to be humans. They fight against this knowledge so hard. They ask for him to stop and Archer leaves Phlox to his work. T'Pol finds an asteroid crash site that explains what happened. It is what caused the rain that nearly wiped them all out.
It seems that the radiation that forced them underground has started to get into their water, it is what caused her cancer. He finds a picture of the old lady when she was a little kid, as a human. Proving that she is a human. Her son tries to get her away from these truths. While the son doesn't want to believe it the mother is starting too. She remembers just a bit of it. Archer freaks out, he can't leave the humans down there to die but they don't want his help. T'Pol suggests using force to move them. Archer says they can't use force he has to get them to agree to it. T'Pol asks if it is the right thing to do, they won't fit in on Earth. The tunnels are their homes, Earth wouldn't be the right fit for them. It would destroy who they are. Archer calls Trip into his office.
The three of them start looking for a new location to move the colony that is outside of the radiation field. Archer goes to take the mother and son back to the tunnels and tries to talk the mother into moving her people to that part of the planet. The son believes that Archer wants their tunnels for himself.
The shuttle lands and falls through the ground. It seems that the tunnel has given way to the weight of the shuttle. The son takes Archer's phaser and leads his mother and Archer to Reed and the others while Mayweather stays with the ship. One of the planets people is pinned in the water below. Archer and the son work together to save the fallen man, going a long way to prove faith in each others people.
The two of them make it down to help the trapped man but he water is getting higher and higher, they don't have much time left. They can't get the tree off of him and Archer asks for his phaser back. The son doesn't trust him at first but Archer talks him into it and uses the phaser to cut the tree in half. They free the man before he drowns. They get him back to camp alive.
Reed isn't doing so well, his wound is starting to get infected. The mother forces her son to tell the others what they have learned. Her son doesn't want to believe it, he just wants to stay and be happy but the mother believes Archer and talks her people into moving onto the other side of the planet.
Mayweather is beyond excited that the crew figured out what happened. Archer lets him put the report together and thus ends the tale of what happens when humans split off from civilization.