The U.S.S. Voyager finds itself under attack by a cloaked vessel. The bridge crew discovers it's an antiquated Klingon battle cruiser, which they can detect with a metaphasic scan. Captain Janeway orders return fire, disabling the vessel's cloak. Janeway hails the damaged ship, telling them to stand down, but Captain Kohlar declares they will not surrender to sworn enemies of the Klingon Empire. Janeway says there's been a misunderstanding since the Klingons and the Federation signed a peace treaty more than 80 years ago. Kohlar does not trust her, so Janeway tells him her Chief Engineer is a Klingon. He wants to meet that Klingon.
Kohlar boards Voyager and meets B'Elanna Torres. He sees that she is pregnant, and asks if the child was conceived during a holy month, which she confirms. Kohlar returns to his ship and tells the other Klingon leaders that the prophecies of the "Scrolls" have come true, and that the "Day of Separation" has arrived.
The Voyager bridge crew realizes the Klingon ship is having a warp core breach. Kohlar requests emergency transport, and all 204 Klingons from the vessel are beamed over into the shuttlebay. Voyager jumps to warp as the Klingon ship explodes. Janeway and Tuvok confront Kohlar with information that he made his ship self-destruct. Kohlar says it was the only way to get them aboard Voyager. He explains that they were following a sacred text that told them to embark on a long journey to find their "Kuvah'Magh" or "Savior." Kohlar believes that savior is the unborn child of B'Elanna Torres.
Janeway briefs the senior staff about the situation and asks them to respect the Klingons and make room for them by having the crew double up on quarters. The Klingons fill the Mess Hall as Neelix provides them meals of gagh, and when a fight breaks out between two of the visitors Harry Kim breaks it up, attracting the attention of a large, lustful Klingon woman. Meanwhile, Torres avoids contact with the Klingons for fear of being ambushed. Some of them start a hunger strike and won't eat until Torres meets with their Council of Elders, so Janeway asks her to cooperate. Torres reluctantly complies, and in the meeting a skeptical elder, T'Greth, realizes she is only half-Klingon and that the baby, with a human father, is also a "mongrel child." Captain Kohlar counters that the signs of the prophecy are there, but T'Greth believes he led them to a false savior.
Later, Kohlar tells Torres that whether or not her baby is the true savior, they must convince his people that she is. He explains that they have been searching for more than a hundred years, and have found nothing but hardship and isolation. He sees Torres and her child as an opportunity to end the wasteful journey. If the Klingons accept her child as their savior, Torres will hold great influence over them and point them toward a home. Torres and Janeway both tell him that they will not deceive his people. So Kohlar suggests that Torres study their scrolls and interpret them in a way that appears consistent with the events of her life, and then they will bring those consistencies to the attention of the council. Otherwise violence could break out.
Torres agrees to help out Kohlar, who makes her realize that the Scrolls can mean anything one wants them to. For example, a "glorious victory against an army of 10,000 warriors" could be interpreted as destroying a Borg vessel, which Torres has helped to do. After spending two days reviewing the Sacred Scrolls, she appears before the Klingon council and tells a spirited story about a heroic encounter with the Hirogen, exaggerating her role in the fight, to the pleasure of the Klingons. She also tells them that Voyager has set course for a planet very much like their homeworld. But T'Greth is still unconvinced, accusing her of saying what Kohlar tells her to. When Torres' husband Tom Paris comes to her defense, T'Greth tests his role in the prophecy by challenging him to a death match. Paris accepts, to Torres' dismay. Janeway refuses to allow such a death match, but at Paris' and Kohlar's urging agrees to a compromise bout where blunted bat'leths would be used and no one would be killed.
Meanwhile, Kim is trying to avoid Ch'Rega, the Klingon woman he restrained earlier and who now wants to mate with him. Neelix helps out by treating Kim with Klingon-style harshness, which causes Ch'Rega to get aroused over the Talaxian instead.
The match between Paris and T'Greth commences in the holodeck. Paris holds his own against his bigger opponent, but he is surprised that T'Greth seems to wear out so quickly. T'Greth collapses, and Kohlar realizes he's come down with the "Nehret," a fatal disease. The Doctor learns that all the Klingons aboard carry the Nehret virus, and have passed it to Torres and her child. Refusing to stay in Sickbay, T'Greth approaches his comrades and declares that since the child has the disease, she cannot be the Kuvah'Magh. They must resume their search, and to do so, they must seize control of Voyager.
The ship arrives at the planet that will serve as the Klingons' new home. Pretending to cooperate with Kohlar, T'Greth asks to beam down as part of the survey mission, rather than to die on Voyager. Kohlar agrees, but T'Greth takes the opportunity, with help from his supporters, to take over the Transporter Room and beam most of the Voyager crewmembers to the surface. Unable to beam out the Bridge crew, the Klingons transport themselves to the Bridge and do battle there with phasers, but T'Greth and his accomplices are eventually knocked out.
T'Greth wakes up in Sickbay and is informed that his illness has been cured — the Doctor has synthesized an antivirus using hybrid stem cells from the unborn mixed-breed baby. T'Greth realizes the child has cured him, and Kohlar declares that she is truly their savior. The Klingons begin to settle on their new homeworld, and Torres accepts a bat'leth from Kohlar, given to him by his great-grandfather, as a gift for the baby. Later, Paris wonders if the child isn't truly the prophesized savior, given the coincidence of the two ships running into each other. Torres doesn't buy it, but she agrees to consider "Kuvah'Magh" as a name for their daughter.