During an away mission, Janeway and Chakotay are bitten by an insect that infects them with an incurable virus. When the Doctor can't treat them, the two officers resign themselves to remaining on the planet, which has an environment that blocks the progression of the terminal disease. After supplies are beamed to them from Voyager, Janeway gives the crew orders to proceed to the Alpha Quadrant and puts Tuvok in command of the ship.
The decision to leave the Captain and First Officer behind weighs heavily on the crew, and they urge Tuvok to rendezvous with a Vidiian convoy, knowing that the aliens' advanced medical knowledge might include a cure for the virus. Tuvok refuses; Janeway has forbidden the crew to contact the untrustworthy Vidiians, renowned for their willingness to murder involuntary organ donors in their ongoing battle against the Phage.
On the planet, Janeway works to develop a cure for the virus while Chakotay tries to make their lives comfortable. After a violent plasma storm strikes the planet and her research equipment is destroyed, she must come to grips with the fact that they are unlikely to ever leave this world. On Voyager, Tuvok realizes that sometimes a Captain must disobey an order for the welfare of his crew. He contacts the Vidiians and asks them to put Voyager in touch with the Vidiian physician Denara Pel, a close friend of the Doctor's. Pel quickly responds and offers to share the cure to the mysterious virus. They arrange a rendezvous for the next day.
As Janeway and Chakotay draw closer to each other, responding to the intimacy of their situation, Voyager goes to meet the Vidiians. But it's a trap, and the ship comes under a punishing assault. In the midst of the attack, Dr. Pel contacts the Doctor and offers the serum. Tuvok is able to drop the shields long enough for them to retrieve it and to eject an antimatter container from the ship. Then they fire a torpedo at the container and the resulting explosion incapacitates the Vidiian ships long enough for Voyager to escape. Tuvok retrieves the Captain and Chakotay, who resume command of Voyager and return to their traditional relationship.