Janeway and Chakotay both contract a deadly virus, and they are forced to remain on a planet where the environment will keep the disease from killing them. Janeway orders Voyager to continue its journey to the Alpha Quadrant, with Tuvok as its new captain. She and Chakotay prepare to spend the rest of their lives alone together on the planet. Janeway explicitly forbids contact with the Vidiians, as they have taken every opportunity to harvest the crew.
Many of the crew, especially Ensign Kim, come to believe that Voyager should contact the Vidiians. The crew does have Torres, whose DNA the Vidiians believe could offer a cure to the Phage, a disease which ravages them. The ship also has the goodwill of the scientist Denara Pel, who had been saved by the ship's doctor. They had also enjoyed somewhat of a romance. Tuvok and Kim argue twice over this course of action, with Tuvok thinking this is illogical. One of the many reasons for this is that Voyager had recently destroyed a Vidiian ship, leading to the loss of hundreds of their people. Kim argues and comes close to being permanently relieved of duty.
Back on the planet, Janeway makes friends with a local monkey-creature and researches potential cures herself. However, a plasma storm soon destroys much of the equipment she would need. Romantic tension develops between Chakotay and Janeway.
Soon, Kes comes to talk to Tuvok in the Ready Room. Tuvok soon realizes, with the presence of many of the crew on the bridge, that changing his mind might be the best thing to do. Voyager contacts the Vidiians, who seem willing to work with them.
However, it is a trap. A large force of Vidiians arrive for battle. Pel herself had created a cure and she contacts the Doctor on his personal channel. With a few split-second maneuvers, the crew manages to transport the cure.
On the planet, well after the debris from the storm had been cleaned up. Janeway and Chakotay are discussing the new vegetable garden. Suddenly their communicators begin to work again. It is Tuvok, many hours away. The two pack up from their new home and return to Voyager. Janeway and Chakotay resume their former professional relationship.