The Caretaker has been providing for the native Ocampa people and their world since his race severely damaged their atmosphere in an accident. Knowing his own death nears, the aged alien is collecting people of different origins to test them for compatible DNA to provide a mate that will bear offspring to carry on his work. The Caretaker kidnaps both crews and examines them, but they are returned some three days later, except for Kim from Voyager and B'Elanna Torres, a half-Klingon, half-human Engineer from the Maquis vessel. Banding together to successfully rescue their missing mates, the two crews encounter Neelix, a Talaxian scavenger and jack-of-all-trades and his lover Kes, an Ocampan who strives for more than her people's sedate and dependent lifestyle underground.

The Ocampan planet also introduces the Federation crew to the Kazon, an alien race on this planet's surface who covets the power and resources -- especially water -- that the Caretaker bestows on the sealed-off Ocampa underground. To save the natives from the Kazon as the Caretaker's death nears, Janeway destroys the Caretaker's power Array -- and her own people's best and perhaps only way home. Deprived of their target, the enraged Kazon are beaten only by a kamikaze run on their mother ship by Maquis Captain Chakotay and his ship, after his crew are beamed aboard Voyager.

Chakotay takes up Janeway's offer to merge their crew under a Starfleet operation; he considers Paris a traitor for helping Starfleet, but he knows Tuvok's undercover work was just following orders. Neelix and Kes convince Janeway of their usefulness and are allowed to stay on board. Chakotay is assigned to be First Officer, and Tom Paris is reinstated to service as a Lieutenant and serves at the Conn. They must all work together to find the way back home.