Stardate 48315.6: The Starfleet ship USS Voyager under the command of Captain Kathryn Janeway sets out to search for a Maquis ship missing in the Badlands. Janeway enlists the help of Tom Paris, a former Starfleet officer who was expelled for causing an accident and who was briefly a member of the Maquis. The Maquis ship, commanded by another former Starfleet officer named Chakotay, was infiltrated by Tuvok, Voyager's tactical officer. However, inside the Badlands Voyager encounters a displacement wave and is dragged into the Delta Quadrant, just as previously the Maquis ship. Janeway's first officer, the helm officer, the chief medical officer, the nurse and the chief engineer are killed in the process. The surviving crew are held prisoners aboard a huge space station. After their release Ensign Harry Kim is still missing, as is B'Elanna Torres from the Maquis ship. They find themselves in the underground city of the Ocampa, suffering from a disease for which the Ocampa have no cure. Following the energy pulses that the station, called the Caretaker's Array, is sending out out, Janeway sets a course for the Ocampa planet. Voyager picks up a man named Neelix, who agrees to help the crew get back their missing people. But as an away team beams to the barren surface with water for the Kazon-Ogla living there, Neelix only cares to get Kes released, an Ocampa who has found her way to the surface and who he has fallen in love with. Kes persuades Neelix to further support the Starfleet crew. They find breaches in the security barrier that protects the Ocampa city from the outside world and beam down. The Caretaker, however, stops supplying the Ocampa and begins to seal the access to the city. The only way back to the surface for the away team, together with Kim and Torres, is through the ancient tunnels. Back at the Caretaker Array, Tuvok and Janeway find out that the Caretaker is dying. His race of extragalactic explorers once caused an ecological disaster on the Ocampa homeworld, and two of them have stayed behind, supplying the Ocampa with energy. The other Caretaker has abandoned her duty. Now that the remaining Caretaker is dying, his only worry is that the Kazon might take control of the Array and its technology, and overwhelm the Ocampa. This is why he activates the Array's self-destruct. Outside the Array a battle with the Kazon ensues, and Chakotay has to sacrifice his ship to disable a huge Kazon vessel. The Kazon vessel collides with the Array, disabling its self-destruct system. Janeway decides against a quick return and destroys the Array. The crews of the Federation ship and the destroyed Maquis ship join in their endeavor to find a way home, which would take 75 years at maximum warp. Neelix and Kes too join the crew of Voyager.

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