In this episode, the Federation starship Voyager, alone in the Delta Quadrant, is lured into a trap which leads to the ship being commandeered by the hostile Kazon who forcibly remove the ship's crew to an inhospitable planet.
Ensign Lon Suder, having been confined to his quarters for life as punishment for his murder of Crewman Darwin, has attempted to make amends for this by making several agricultural-advancements. Suder is happy that his work might benefit the crew as he can improve the garden which produces most of the rations for the crew. His homicidal tendencies seem to be well under control by the use of Vulcan mental disciplines learned from Tuvok. Seska calls Voyager stating that Commander Chakotay must rescue her and her baby, now that she gave birth, since Culluh saw that the child was not his. Captain Janeway and Chakotay argue on whether or not to save his son, whether its a trap or a real plea for help. In the ready-room, everyone thinks up ideas to fight the Kazon in the event of a trap.
An apparent defector of the Kazon is soon found on a stranded ship and taken on board to Sickbay, and explains his predicament, although Chakotay remains suspicious - especially when he mentions Seska's death. As Voyager travels further into Kazon space, facing heavier attacks that seem focused at the same general area of the ship, the man commits suicide in a grisly and violent explosion, which severely damages Suder's quarters and disables several of Voyager's systems. As Voyager is overwhelmed by the Kazon, Lt. Paris takes a shuttle to find a Talaxian colony for aid. Voyager is boarded and taken over by Kazon forces. Captain Janeway attempts to activate the ship's self-destruct sequence to prevent the Kazon from taking the ship, but important systems ("Secondary Command Controls") had been damaged from earlier Kazon skirmishes, disabling this ability, revealing the true strategy of the Kazon.
The crew is marooned on a barren planet inhabited by primitive but seemingly hostile natives. Only two crew members are left on board Voyager - the Doctor and Suder, who was presumed dead in the explosion. Suder hides in the vents and Jefferies tubes of the ship, risking his sanity after he is forced to kill a Kazon soldier. His old Maquis tricks keep him from being detected, but also alert Seska, who has similar experience. The Doctor takes the "credit" for the dead Kazon soldier and stops Suder from being detected. Seska doubts the story, but deactivates the Doctor's program just in case.
Meanwhile, on the planet, crewman Hogan is devoured by a gigantic worm creature.[notes 1] The natives of the planet kidnap Kes and Neelix. Chakotay attempts to negotiate for their return, but this does not go well and he, Kes and Neelix plus other crewmen flee and are forced to hide in one of the caverns that the giant worm lives in. The natives attempt to smoke them out with a fire.
Back at camp, things are going wrong, although the crew have managed to find food and warmth. Ensign Wildman's baby falls ill and continues to get worse and Chakotay's team is still missing. Janeway gathers her own crew to search for Chakotay. Inside the caverns, a mis-step leads to a crew member waking and getting eaten by the worm. Outside, Janeway has Lt. Torres and two others draw off the natives with a distraction. It works, allowing them to put out the fire and get the rest of the crew out. The worm ends up buried under tons of rock dislodged by Tuvok and others as they escape.
Suder and the Doctor risk their lives to repel the Kazon. Suder, under orders from Tom Paris, who is with a Talaxian convoy, attacks the engineering section of Voyager. His goal is to sabotage the phaser weapon systems. He succeeds, but is shot in the back by a dying Kazon and dies moments after. The Kazon then attempt to destroy Tom Paris' shuttle but the sabotaged phaser coupling overloads, killing most of the Kazon and so they decide to abandon Voyager. Seska herself has been mortally wounded; she stumbles into Janeway's ready room and dies next to her child, who survived. Maje Culluh, one of the few survivors of the attack, momentarily grieves for Seska, and then takes the baby and leaves.
On the planet, volcanic eruptions have forced the Voyager crew and the natives to move out together. Chakotay gains the respect of the natives when he rescues one of their children from a lava flow. The leader of the tribe gathers together plants that help Ensign Wildman's baby to recover. The crew and the natives both watch in bewilderment as Voyager descends to the planet to pick them up. Tom Paris greets Janeway and the crew on the bridge and explains of Suder's deeds. In Sickbay, there is a brief conversation over the bodies of Seska and Suder; Tuvok wishes for Suder the peace he had not been able to gain in life. Voyager continues on the journey home.
^The discovery of the remains of crewman Hogan's uniform by an alien species the Voth serves as a starting point for the plot of the later Voyager episode "Distant Origin" (Season 3 Episode 23).
Martha Hackett whose character Seska is killed off this episode, received two copies of the script; the first where Seska survived, but her baby died and the second as was aired. She was only told that Seska was to die less than a day before filming. She would return to play the character twice more in the series.