In the late 24th century, a renegade group known as the Maquis operate outside the law to right what they see as Federation injustices. After infiltrating a Maquis cell to apprise Starfleet of the group's activities, Lieutenant Tuvok, along with the crew of a ship commanded by the Maquis captain Chakotay, disappear in an area of space known as the Badlands. Tuvok's commanding officer, Captain Janeway, leads a mission to find the Vulcan lieutenant, enlisting the aid of Starfleet prisoner Tom Paris, a former Maquis member, to guide her ship, the U.S.S. Voyager NCC-74656, through the Badlands.
Considered a traitor by most of Voyager's crew, Paris strikes up a friendship with Ensign Harry Kim, a naive young Starfleet Academy grad. Kim learns that Paris was drummed out of Starfleet after his piloting error caused the deaths of three officers. The outcast joined the ranks of the Maquis, but was soon arrested by Federation authorities.
After reaching the Badlands, Voyager encounters an inexplicable phenomenon that sends the ship hurtling to the Delta Quadrant, located 70,000 light years from home. The catapult effect kills a number of crewmembers, including the Chief Medical Officer, who is replaced by an Emergency Medical Hologram (EMH) that attends to the wounded. But the EMH has barely begun his work when the entire crew of Voyager is transported to what appears to be a pastoral farm, populated by friendly humans. But it's only an illusion; the farm is actually the interior of the Array, a huge space station, and the residents are holograms. The crew is imprisoned within a strange laboratory facility, alongside the missing Maquis.
After being subjected to a painful examination, the crews of Voyager and the Maquis vessel are returned to their respective ships, docked outside the Array. But two crewpersons are missing: Harry Kim and B'Elanna Torres, the half-Klingon, half-human engineer from the Maquis vessel. Returning to the "farm," Janeway confronts the only remaining inhabitant, an old man playing a banjo. But the man cares nothing about their dilemma and offers them no information about the missing officers.
Noting that the Array is sending energy pulses toward the fifth planet of a neighboring system, Janeway sets course in that direction. Far beneath the surface of that planet, an ailing Kim and Torres regain consciousness in a medical facility. But what they're doing there — and why — they have yet to discover.