An antique Klingon D-7 class ship attacks Voyager, cloaked. Using a metaphasic scan, Seven of Nine calculates the position of the ship, allowing Tuvok to fire on the ship, disabling their cloaking device. The captain of the Klingon ship, Kohlar, refers to the Federation as "sworn enemies of the Empire." Naturally, Kohlar doesn't believe Kathryn Janeway when she says that the Federation and the Empire have been at peace for eighty years. When he sees B'Elanna Torres, who is pregnant, he changes his mind. He has his crew fake a core breach on his ship so that all the Klingons aboard are transported to Voyager. When he was confronted by Janeway about this, he explains that he believes Torres's unborn child is the prophesied "Kuvah'magh," the savior of the Klingon people, the one whom Kohlar's ancestors left the Klingon world in a multi-generational voyage in order to meet. The elder Klingons are very skeptical, especially because Torres is only half Klingon and her daughter is only quarter Klingon. Other Klingons constantly pursue Torres when she is working, prompting her to beam from place to place.
T'Greth challenges Tom Paris, B'Elanna's husband, to a duel to the death, which Paris accepts. At Janeway's insistence, however, T'Greth and Paris agree to a non-lethal duel with blunted bat'leths. To everyone's surprise, T'Greth loses the duel.
It turns out that T'Greth suffers from a seemingly incurable disease known as Nehret, which afflicted all Klingons aboard Kohlar's ship, and now Torres and her unborn child as well. T'Greth convinces some of the other Klingons to take over Voyager. After much fighting, the crew retakes the ship. The Doctor then comes up with a cure by using stem cells from B'Elanna's baby.
The Klingons relocate to an M-class planet while Paris and Torres agree to consider "Kuvah'magh" as a possible name for the baby.
The subplot concerns Harry Kim not wanting to mate with Ch'Rega, a Klingon woman who lusts after him because he broke up a fight between her and another Klingon over food. However, he is not attracted to her in return. Neelix offers to take her off Harry's hands. Harry pretends that Neelix beat him handily in a physical fight, and Ch'Rega is most impressed. Neelix and Ch'Rega copulate in Tuvok's quarters, leaving the place an utter mess. Tuvok tells him to get out after seeing the destruction.