The USS Voyager is launched from Deep Space Nine and ordered in to the Badlands to find a missing Maquis ship. Upon entering the Badlands, Voyager is struck by massive displacement waves, wreaking havoc on the ship. When the crew recovers they find themselves in the Delta Quadrant, over 70,000 light years from Federation space. A number of the crew are dead, including the second-in-command, helm officer, and chief engineer; the medical staff are also dead, forcing the crew to rely on the Emergency Holographic Doctor for aid. However, before they get their bearings, they are brought aboard a nearby array by the "Caretaker". Aboard the array, the crew see through a holographic simulation and discover the Maquis crew, unconscious and undergoing strange medical experiments. Before they can react, the Voyager crew are also subjected to the same experiments. Later, both crews recover consciousness and find they are each missing one crew member; Harry Kim from Voyager, and the Maquis B'Elanna Torres. Further attempts to negotiate with the Caretaker are fruitless as he insists there's no time for such talk. Captain Janeway offers to work with the Maquis leader Chakotay to unite their crews to find their missing persons and return to the Alpha Quadrant.
The two ships follow pulses of energy sent from the array to a nearby arid planet. En route, they encounter Neelix, a space trader who is eager to help them out in exchange for helping to rescue his companion, the Ocampa Kes, from the violent Kazon which inhabit the planet's surface. Kes explains that her people live in an underground complex beneath the surface, and are cared for by the Caretaker who supplies them with energy, with the only expectation in turn that they care for the beings that he sends to them, each who are infected with a strange disease that appears incurable. As the crews determine how to rescue Kim and Torres, the Caretaker moves the array closer to the planet and begins firing more lethal bursts of energy. Tuvok determines that the Caretaker is dying, and is making sure that the Ocampa are kept safe by destroying the only means of access into the complex. With time running short, a combined away team is able to penetrate the shields protecting the complex and rescue Kim and Torres.