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Following on from "The Poison Sky", the TARDIS takes the Doctor, Donna and Martha to the planet Messaline, where armed men working for General Cobb (Nigel Terry) seize the Doctor and stick his hand in a cloning machine, which uses his diploid cells to produce the titular character, Jenny. She is "born" an adult soldier trained to fight against the Hath — militaristic, fish-based creatures who communicate through bubbles. During a battle with the Hath, the Doctor and Donna are separated from both Martha and the TARDIS.

Martha befriends the Hath, who do not speak in any understandable fashion, while the Doctor and Donna learn about the history of the planet from the humans. The two races were initially meant to live in peace in a colony, but have long been at war, which the humans claim the Hath started. Donna notices a recurring series of plaques with eight-digit codes on them. While examining a electronic map terminal of the structure, the Doctor reveals a secondary set of blueprints leading to a structure the humans refer to as the temple of "the Source", the breath of their goddess. Believing this to be a weapon, Cobb intends to use it to wipe out the Hath, and has the Doctor, Donna, and Jenny locked up when the Doctor protests. The Doctor's actions have likewise altered the Hath's map terminal, and they too set out to find the Source.

While the Doctor is initially dismissive of his so-called daughter, Donna uses a stethoscope to confirm that Jenny has two hearts, and the Doctor comes to see many of his traits in her. Jenny, for her part, is puzzled by the Doctor's insistence that he isn't a soldier, despite his obvious aptitude for it. He explains that he was a soldier once, in a much greater war, and warns Jenny that once she starts killing it'll become addictive. Jenny distracts the guard and springs the trio from their prison cell. The Doctor, Donna and Jenny set out to beat the humans to the Source, while Martha opts to take the surface route with a Hath she has befriended. She manages to reach the temple first, but her Hath friend dies when he saves her from some quicksand.

The Doctor's party reaches the temple shortly after and the two sides join once more. The Doctor discovers that the temple is in fact a colony ship. Donna, while studying a number display matching the plaques, realises that they are a dating system, and according to the display, it's only been a week since the war started. The logs indicate the commander died and the resulting power vacuum started the war. Because the cloning machines produce new soldiers so quickly, they ran through dozens of generations in only a week, degrading their history to mere myth in a relative instant. They move further into the ship, where they find a terraforming agent, the Source, ready to be released.

The two camps converge on the Doctor's party, where he explains to them what has happened. He releases the terraforming agent and all but Cobb drop their weapons; Cobb instead tries to shoot the Doctor. Jenny steps into his path and is shot in one of her hearts. Jenny apparently dies in the Doctor's arms. The Doctor holds Cobb at gunpoint but does not pull the trigger, saying, "I never would", and tells both sides to make that the basis of their society. The new colony offers to bury Jenny as a start.

In the TARDIS, the Doctor concludes that the entire event was a ontological paradox; the TARDIS sensed Jenny but arrived too early, allowing her to be born in the first place. He returns Martha home, and Donna resolves to stay with the Doctor while Martha leaves. Meanwhile, Jenny revives in front of Cline and a Hath, after exhaling a coloured gaseous substance. She escapes Messaline in a spaceship while resolving to fight villains, inspired by her father.

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