Tom Paris and B'Elanna Torres are in the middle of a heated argument when they are interrupted by the appearance of a stranger, who has just materialized in front of them out of nowhere. They escort him to Sickbay, where all they can figure out about him is that he is much more sensitive to light and cold than are humans. The stranger, Dammar, seems just as confused as they are. Then they realize that someone is missing from Sickbay. Kes is nowhere to be found and a quick check with the computer reveals that she disappeared off the ship at precisely the same time as Dammar showed up.
A short time later, Harry Kim disappears and is replaced with someone in similar garb as Dammar. They are Nyrians, and more of them appear as Voyagerâs crew blinks out, one by one, at an interval of nine minutes and twenty-two seconds. At this rate, Voyager will be emptied of her crew and filled with Nyrians in less than a day. The aliens seem nervous and puzzled, but they assist the crew with the information they have.
Eventually the ship is overrun with Nyrians and only a skeleton crew remains. Torres is still on board, furiously working to figure out the problem. A Nyrian scientist works with her in Engineering, both watched by a Voyager security officer. As Torres comes close to discovering what's going on he pulls a phaser on her, stuns the guard and with a few quick keystrokes, he transports Torres off the ship. She materializes in a sunlit garden compound where most of the Voyager crew is milling around, not sure what to do. Captain Janeway confirms that the Nyrians are responsible for their predicament. After the injured security officer is found in engineering, Chakotay discovers the Nyrians are trying to take over the ship. He orders the remaining dozen crewman to fortify the bridge and engineering, but they are quickly overrun. Chakotay and Crewman Genaro (the last two Voyager crew members aboard) attempt to sabotage Voyager, and are successful in disabling warp drive. Genaro vanishes like the rest. Chakotay downloads The Doctor to his mobile emitter before he too is transported to the compound and the Nyrians take over the ship.
A Nyrian spokesperson, Taleen, informs the crew that they are now in their new permanent home and Voyager will be added to the Nyrian fleet. They have a policy of hijacking vessels and colonies in this manner, transporting their populations to compounds specially designed for the comfort of their unique residents.
The crew discovers that the compounds are interconnected when a pleasant yet timid alien called Jarlath walks through a portal from his home compound. A few adjustments to The Doctor's mobile emitter allows him to scan for other portals, and four of the crew go to explore the corridors behind them. Paris and Torres find a number of doors leading to other environments, including a steamy jungle, a volcanic wasteland, and an icy snowscape. A Nyrian patrol surprises them, and they escape into the ice planet habitat. The cold-sensitive Nyrians chase them in, but don't last long in the snowstorm.
Janeway and Tuvok access a database that lists all of the habitats and provides a map: the environments are just big rooms on board a massive starship. They figure out the mechanism that allowed the Nyrians to swap Voyager`s crew with their own. Using it, they transport the half-frozen Torres and Paris back to the Earth habitat, and replace them in the ice caves with Dammar and Rislan, the Nyrian ship hijackers. They are horrified to find themselves in such a frigid environment and agree to give Janeway back her ship. She arranges trips home for all the displaced populations held on the Nyrians' ship.