Janeway and Chakotay both contract a deadly virus from a wassoop-insect, and they are forced to remain on the planet below where they contracted it with the environment keeping 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.
Back on the planet, Janeway makes friends with a local monkey-creature and researches potential cures for herself and Chakotay. Chakotay states that since a cure couldn't be found by the Doctor, they should stop and enjoy the time they have left; but, Kathryn refuses. However, a plasma-storm soon destroys much of the equipment she would need. Romantic tension develops between Chakotay and Janeway.
Many of the crew, especially Ensign Kim, come to believe that Voyager should contact the Vidiians. The crew does have Torres, whose DNA possesses an incredibly powerful immune system, in which the Vidiians believe could offer a cure to the Phage (a disease which has ravaged them for centuries). The ship also has the goodwill of the scientist Dr. Denara Pel, who had been saved by the ship's doctor; they 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 three hundred of their people. Kim argues and comes close to being permanently relieved of duty. The next day, 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 with a large force of Vidiians arriving 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 badge-communicators begin to work again. It is Tuvok, who is still many hours away. Eventually, the two pack up from their new home and return to Voyager, resuming their former professional relationship.