The USS Voyager beams aboard three people just before their damaged ship explodes: an Ilari female named Nori, her injured spouse Tieran and an Ilari male named Adin. Although the Doctor and Kes try to save him, Tieran dies. Not long after, Neelix is shocked when Kes announces she'd like to spend some time apart from him. When Voyager arrives at Ilari, the local leader, known as "the Autarch," sends a representative to the ship instead of coming himself. Inexplicably, Kes pulls out a phaser, kills the representative and a crewmember, and escapes in a stolen shuttlecraft with Adin and Nori.
Kes takes the shuttle to a military encampment and takes command of the waiting troops. In the meantime, Janeway meets with Demmas, the Autarch's oldest son, who explains that Kes' body is now inhabited by Tieran, a former Ilarian ruler who was overthrown by Demmas' ancestor 200 years ago. Since then, Tieran has lived on by transferring his mind to a series of host bodies. Janeway agrees to help Demmas stop Kes/Tieran, but before she can, the tyrant has killed the Autarch in front of Demmas' younger brother, Ameron, and appointed himself the new Autarch.
Kes/Tieran tries to poison Ameron's thoughts against Demmas and urges him to cooperate with the new regime. In the meantime, the Doctor designs a synaptic stimulator that will remove Tieran's neural pattern from Kes—if they can get close enough to use it. Tuvok beams into the Autarch's palace, but is caught and imprisoned before he can succeed in the attempt. When Kes/Tieran interrogates Tuvok, the Vulcan is able to initiate a mind-meld and speak directly to Kes, who tells Tuvok she is fighting Tieran for control.
Kes/Tieran orders Voyager to leave orbit, but the stress of the mental battle between Kes and Tieran results in a paranoid Kes/Tieran killing Adin. To Nori's chagrin, Kes/Tieran announces she's marrying Ameron. Moments later, a coalition of Voyager's crew and Demmas' forces bursts into the palace. Paris releases Tuvok, while Neelix places the synaptic stimulator on Kes/Tieran. Tieran jumps to a new host body—Ameron—but Kes places the device on him and Tieran is finally destroyed. Demmas, the rightful heir, becomes Autarch.