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Janeway grows concerned when B'Elanna, Paris, and Lieutenant Peter Durst fail to report in for beam-up after an away mission. In reality, the phage-plagued Vidiians are kidnapping visitors and masking the landscape to cover their operation on the planet. The scientist Sulan is in search of a cure for the deadly disease of his people. During an experiment, B'Elanna is literally split into two separate beings -- one fully Klingon, the other fully human -- by Sulan, who believes Klingons may be immune to the phage. Since the Vidiians are too weak to do their own labor, the unused hostages including Paris, Durst and another Talaxian are put to work digging tunnels.

Sulan is excited when the Klingon B'Elanna shows signs her body is fighting the disease. He wants to replicate her DNA and integrate it into that of Vidiians, telling her she will be considered a hero to his people. But the Klingon B'Elanna suspects that Sulan's interest in her has grown beyond scientific curiosity.

In the prisoner barracks, Paris is shocked when the all-human B'Elanna appears, explaining what has happened. She admits she should be happy at losing her despised Klingon heritage -- growing up on Kessik IV with her mother as the only Klingons, she decided her human father left them because she looked too alien -- but now she realizes the benefits of her Klingon blood.
Meanwhile, an away team led by Chakotay realizes this planet's caves show traces similar to the Vidiian caves previously encountered, and after trying to phaser through a suspected false wall they beam out quickly before two Vidiians who suddenly appear can subdue them.

The Klingon B'Elanna tries to tempt Sulan into freeing her to explore her sexual side, but despite herself she can't hide her revulsion at his patched-together form. He can't help but notice her reaction and promises her that one day his people will be beautiful again with her help. He has Durst killed so his face can be grafted over his own garish features. Instead of attraction, the sight so enrages the Klingon B'Elanna that she breaks away and grabs Sulan, almost snapping his neck. Only the sound of voices sends her from the room, and she eventually helps to plan an escape with her human half and Paris.

Along the way, the B'Elanna halves learn to appreciate each other and, thanks to help from the returned Chakotay in Vidiian disguise, they subdue Sulan and disable the caves' forcefield to beam out. But Sulan gets off one more shot, aiming for the human B'Elanna but killing his beloved Klingon when she steps in to take the hit. The Klingon part dies after beam-up, but the Doctor is able to return enough DNA to restore B'Elanna to her newly appreciated wholeness.