Voyager's crew is surprised when sensors pick up a transmission from someone using a Federation signal. Janeway lays in a course toward the signal, but when they arrive, they're attacked by a Kazon vessel, which seems to know how to penetrate Voyager's shields. Intruders manage to gain access to the starship, steal a transporter module and beam away to their own ship. Janeway informs the Kazon leader, Culluh, that the module is useless without Federation know-how, but Culluh reveals his trump card: he's joined forces with Seska, a former crewmember and Cardassian spy.

The implications of Seska's alliance with Culluh are clear — the Kazon now have an adviser with Starfleet, Maquis and Cardassian tactical experience. Culluh plans to use the stolen module to persuade rival sects to help him conquer the Federation ship. Chakotay tells Torres he feels responsible for Seska's actions because he recruited her into the Maquis, and later he decides to leave Voyager to go after the device on his own.

Chakotay is able to beam undetected from the cockpit of his shuttlecraft to the Kazon bridge. There, he destroys the stolen module but is quickly captured and tortured for Voyager's command codes, which he refuses to reveal.

When Voyager arrives on the scene, the Kazon Majes he's gathered order Culluh to use the command codes to obliterate the starship, but it soon becomes obvious that he doesn't have them. Seska's quick thinking prevents Voyager from beaming Chakotay off the Kazon ship, so Janeway transports the Kazon Majes instead. They agree to release Chakotay and his shuttlecraft in return for their freedom. Later Chakotay is stunned when Seska informs him that while he was unconscious, she extracted some of his DNA and impregnated herself with his child.