After a Maquis space ship that is being pursued by the Cardassian disappears after escaping into a plasma storm within the Badlands, Starfleet set up an inquiry. Captain Kathryn Janeway is tasked with investigating the disappearance of the craft. She puts together a crew that she believes is the best for the job. One of the crew is Tom Paris, a starfleet officer who has been sentenced to prison on New Zealand after being caught joining the Maquis. Her ship, Voyager enters the plasma storm and also disappears.
Voyager disappears like the Maquis ship. Voyager arrives above a desert planet beside a massive space station called an Array and the missing Maquis ship. The ships Doctor is killed so they need to rely on the services of the Medical Holographic Doctor. The station begins to scan the Voyager. As it does so, crew members disappears off the ship. Janeway, Paris and Kim also disappear but reappear in a Redneck country garden house. When Paris and Kim enter a place they shouldn't they are attacked. When Janeway confronts one of the Rednecks, the whole masquerade is revealed. She is shown a large corridor where her crew members and those of the Maquis ship are in a state of unconsciousness.
Janeway and most of her crew wake up onboard the Voyager. She makes contact with the Maquis ship and they meet and agreed a course of action. Janeway, Chakotay and Paris beam aboard the space station and confronts an old man to find out the truth of what is been happening. After a conversation where Janeway are unable to get any answers, he sends them back to the Voyager and breaks off any attempts to communicate with him.
Kim and Torres wake up in a hospital room but their attempts at escaping fail.
Voyager examines the station and notices that beams of light are being sent to the fifth planet in that solar system. They also discover a ship with an inhabitant onboard amongst a graveyard of ships. They make contact with the inhabitant. He explains about the station and the planet. He offers to help in exchange that he comes aboard. Janeway accepts. He identifies himself as Neelix, a Talaxian.
Torres wakes up and after a short fit of anger, calms down so that Kim can talk with her. One of the Doctors in the hospital arrives and talks with them, inviting them out of the hospital and into the city. The Doctor explains to Kim and Torres about their situation, about living underground and how they got their with the Caretaker.
After Neelix has a bath, he accompanies Janeway, Tuvok and Chakotay to the planet. They land just outside city. When they enter the city, they come across a Kazon party. Their first meeting is friendly, the Kazon leader explains to Janeway how he sees the situation after being given some water. When the leader is not concentrating, Neelix takes the leader captive and forces them to surrender. In the melee, the voyager crew escape along with Neelix's girlfriend Kes, an Ocampan
Janeway asks Kes about the city in the medical bay accompanied Neelix and Chakotay. She takes them down to the city as the beams from the Caretakers station increase in intensity. They are confronted by some Ocampans who are not willing to help. Whilst they are searching for Kim and Torres, those two have found an exit to the surface. The Caretaker increases the beams to the planet, rocking the planets foundations. Paris locates the two people they are searching for and goes after them, up a number of flights of stairs. At the top of the stairs is a beam to stop people from getting in or out of the base. They all make it through onto the desert above. Paris and Neelix returns to Janeway whilst the others are beamed aboard the Voyager. Paris helps Chakotay who is trapped. Onboard Voyager, Janeway opens communications with the Kazons but they don't come to amicable agreement and start fighting. Janeway boards the Caretakers space station to discuss how to get home. He won't help and Shes doesn't want the station falling into the Kazon's hand so she destroys the station using the Maquis ship.