A Nyrian named Dammar suddenly appears on Voyager, asking why he's been abducted. The crew isn't responsible for beaming him aboard, and they soon discover that Kes mysteriously vanished from the ship at the same instant Dammar arrived. Not long after, Kim disappears as another Nyrian turns up. Soon, Tuvok also vanishes. After 22 Nyrians take the place of crewmembers, Janeway realizes that they are replacing her entire staff at nine-minute intervals.
Twelve hours later, the bizarre exchange has claimed half the crew. Rislan, a Nyrian astrophysicist, works with Torres to find the cause of the problem. But when Torres catches on to the fact that the Nyrians are responsible, Rislan sends her to an idyllic prison colony, where she finds her fellow crewmembers.
On Voyager, Chakotay comes to the conclusion, too late, that the Nyrians are trying to take control of the ship, and he's transported to the colony. Taleen, a Nyrian spokeswoman, explains that her people steal ships and space stations by gradually replacing their crews; it's less violent than war. The prisoners are then relocated to surroundings that approximate their native environment.
As they try to find a way out, they meet Jarlath, another prisoner, who reveals that different areas of the colony are connected by disguised portals. Torres reconfigures the Doctor's optical sensors so that he can detect the passages. He locates a portal that leads to a network of access tunnels, each, in turn, leading to a different biosphere. Janeway finds a control panel that provides access to the translocation system that brought them to the colony.
The Nyrians detect the crew in the passages and send guards to capture them. Torres and Paris slip into an arctic environment and when the Nyrians, who are highly sensitive to cold, follow them, they're easily incapacitated. Meanwhile, Janeway takes control of the translocation system and beams Dammar and Rislan into the cold environment. Overwhelmed by the freezing temperatures, the Nyrians surrender Voyager. With the ship back in her control, Janeway leaves the Nyrians in a section of their own prison while she helps the other prisoners get back to their own homes.