Now that the U.S.S. Voyager has established two-way communications with Starfleet, Captain Janeway receives her first official assignment in seven years: Locate and retrieve the Friendship 1, a probe launched from Earth in 2067 with a message of peace to other worlds. Contact was lost 130 years ago, but its known trajectory would place it in the Delta Quadrant near Voyager's current position. After five days of searching, the probe is detected on a planet darkened by a nuclear winter caused by antimatter radiation.
An away team consisting of Tom Paris, Harry Kim, Chakotay, Neelix and Lt. Joe Carey take the Delta Flyer to the planet, who go searching for the probe wearing environmental suits. While Paris, Neelix and Carey follow their tricorder readings into a cavern, Chakotay and Kim are surprised to find a field of missile silos containing active warheads. Paris, Neelix and Carey see evidence that the cavern is inhabited, but sensors have detected no lifesigns. They find a piece of debris labelled "Friendship 1" and prepare to transport it to the Flyer, but then are suddenly surrounded by armed aliens who are cloaked in heavy robes and breathing equipment. Meanwhile Chakotay and Kim discover the Flyer has been invaded by one of the planet's inhabitants, who attacks them but then gets knocked out by Chakotay's phaser. Then antimatter weapons start rocking the Flyer, so Chakotay is forced to fly it back to Voyager, leaving the others behind. In the cavern, the native people show themselves to be highly malformed and mottled from radiation exposure, and their leader, Verin, is very hostile to the away team. When Verin learns they're here to retrieve their probe, he accuses them of causing his people's suffering.
Verin contacts Voyager and tells Janeway he's taken her crewmen hostage, demanding the relocation of his people to another planet starting in three hours. Janeway confers with the Doctor, who has examined the unconscious alien Chakotay brought back, and learns that his tissues are saturated with antimatter radiation, explaining why no lifesigns were detected on the planet. The Doctor wakes the alien, named Otrin, who reveals that his planet's devastation was caused by an antimatter containment failure. And he blames the human race for it because until the Friendship 1 arrived and introduced that technology, his people had never conceived of anything like antimatter. After decades of suffering, they came to the conclusion that humans intended to contaminate their world so they could eventually come and conquer it.
Tuvok locates a class-M planet 132 light-years away, and determines it would take almost three years to completely relocate all 5500 of the aliens. Meanwhile Seven of Nine extracts nanoprobes from her bloodstream so the Doctor can reprogram them to cure Otrin of his radiation sickness, and Janeway asks Otrin to elaborate on his efforts to neutralize the planet's radiation. On the surface, Neelix tries to tell Verin that humans are not so bad and never meant to harm his people, but he remains unconvinced. Janeway later contacts Verin and tells him that relocation is impractical, offering an alternative: help Otrin carry out his theories on how to counteract the radiation. Verin won't budge on his demands, so Janeway asks to exchange a supply of food and medicine for one of the hostages. Verin picks out Carey and tells him to set up the transport enhancers. Just before Carey is beamed out, Verin shoots him in the heart and he arrives in Sickbay dead.
Janeway tells Verin she will start evacuating his people in an hour, but then she calls Tuvok and Chakotay into a meeting. In Sickbay, Otrin is getting much better after his nanoprobe treatment, and hopes that Voyager can heal all his people. But Seven points out that Verin has refused their help, and suggests to Otrin that he would be a better leader than Verin. Meanwhile Paris helps a woman on the surface deliver a baby, which arrives stillborn, but Paris is able to bring it to life. Just then a patrol captures another Voyager crewmember, Tuvok, making Verin believe he has another hostage. But it turns out one of the alien guards is the Doctor in disguise, and he helps Tuvok overpower the captors. The hostages can now beam out, but before leaving, Paris tells the new mother the baby won't survive without further treatment, so she lets him take her son to Voyager.
Once the baby is stabilized, Janeway plans to send him back along with some food and medical supplies, but then leave. Paris and Neelix appeal to the Captain to help these people in spite of their refusal to cooperate. So Janeway and Seven work with Otrin to develop a plan to neutralize the planet's radiation with an isolitic chain reaction, using photon torpedoes to deliver the catalytic agent. Otrin brings the now-healthy baby back to the surface and confronts Verin to accept Voyager's help and begin trusting them. Meanwhile the ship enters the planet's atmosphere to detonate the charges that will counteract the radiation. When the ground begins to shake, Verin arms an antimatter missile and prepares to launch it at Voyager. But his own lieutenants — and the grateful mother — aim weapons at him to prevent him from ruining their only chance for survival. Verin realizes Otrin is in command now. Just then a child runs in and urges everyone to come outside. They see that sunlight is starting to break through the dark clouds, for the first time in decades. Voyager retrieves the Friendship 1 and resumes course for the Alpha Quadrant, but the success of their mission cost them the life of a crew member.