While routinely exploring a new planet for foodstuffs, a cloaked Kazon-Nistrim ship is detected in orbit. Therefore, the Away Team is recalled but Chakotay can't find Seska. He locates her in a nearby cave, hiding from two Kazon. She had been gathering mushrooms and wandered from the group. Chakotay is hurt in the exchange of fire but Seska gets them both beamed aboard safely.
Rejecting Neelix's choice of foods and recipes, Seska and some other Maquis later break into the food reserves and steal the mushrooms she found to make mushroom soup. She privately brings a pot to the recuperating Chakotay, but the romantic mood between the former Maquis lovers is broken when Neelix reports the break-in. Chakotay angrily reprimands everyone involved, including himself as an accessory. Seska is stunned at his reaction and leaves, teasing him that her eye is now on Kim.
Three days later, the U.S.S. Voyager gets a distress call from a Kazon warship. It turns out to be the one they just encountered, but with only one survivor amid devastation that was caused by Federation technology. Someone on Voyager had to have given them the technology.
Against orders, Seska beams aboard the Kazon warship to retrieve the Federation equipment and is injured. In Sickbay, a routine blood test reveals racial factors of Cardassian origin, not Bajoran, but she explains a bone marrow transplant from a Cardassian woman caused the change during a childhood case of Orkett's Disease.
Another Kazon ship responds to the distress call, and Janeway allows visitors for the ailing Kazon. But the Maje and his aide kill him and an angry Janeway sends them back, ignoring their claims to the damaged ship so it can be checked further for clues. Seska and Carey are now suspects in the espionage because the technology was sent from an Engineering station they both had access to. B'Elanna Torres retrieves the device from the wrecked vessel: a simple food replicator that rejected a Kazon interface with disastrous results.
Chakotay and Tuvok set a trap to find the guilty Engineer — finally revealed to be Seska. She is indeed a cosmetically altered Cardassian who had rejected Janeway's nobility and instead sought allies among the powerful Kazon with the gift of technology. Before she can be arrested, though, Seska beams herself aboard the departing Kazon ship.
Somewhat shaken by the turn of events, Chakotay ruefully wonders aloud about his old Maquis crew: if Tuvok spied for Starfleet and Seska was a Cardassian, was anyone aboard working for him?