We Surrender

The TARDIS is drawn to the planet Messaline, materialising in an underground tunnel. The Doctor, Donna Noble and Martha Jones soon discover that they have arrived in the midst of a war which has been waging for generations between human colonists, lead by General Cobb, and the Hath - militaristic, fish-based creatures who communicate through bubbles.

The human colonists 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. The Hath then appear and a battle commences leading to the tunnel they are in being sealed off. However, this causes The Doctor and Donna to become separated from Martha and the TARDIS by the rock fall.

Martha befriends the Hath, while The Doctor and Donna learn, from the human colonists, more about the cloning and the history of the planet. It seems that the two races were initially meant to live in peace in a colony, but have long been at war.

Jenny is 'Born'

While examining an 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 announces that he intends to use it to wipe out the Hath. When The Doctor protests he has The Doctor, Donna, and Jenny locked up. However, unbeknown to them The Doctor's actions have likewise altered the Hath's map terminal, and they too set out to find The Source.

While imprisoned together Donna proves to The Doctor that Jenny is a member of his own race as she has two hearts. Jenny though is puzzled by The Doctor as he has the aptitude to be a soldier, despite his insistence that he is now one. He does though warn Jenny that once she starts killing it'll become addictive.

Jenny

The Doctor, Donna, and Jenny finally manage to escape from the cell, when Jenny distracts the guard, and they set out to beat the humans to The Source. Meanwhile Martha is also trying to reach The Source. She though goes above ground 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 plaques that she has spotted previously within the colony, realises that they are a dating system, and according to the display, it's only been a week since the war started. The Doctor deduces from the ship’s logs the war started when their commander died resulting in a power vacuum and that 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 short time.

As they move further into the ship they find a terraforming agent - The Source - ready to be released. It is then the human colonists and the Hath catch up with them. The Doctor manages to persuade them not to fight and explains to them what has happened. It is then that he releases the terraforming agent. Despite the Hath and the human colonists dropping their weapons Cobb instead tries to shoot The Doctor. However, Jenny steps into his path and is shot instead. Enraged at this pointless death The Doctor nearly shots Cobb but he does not pull the trigger.

Cobb

Back 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, back on Messaline, Jenny suddenly is revived, after exhaling a coloured gaseous substance, and escapes the planet in a shuttlecraft resolving to fight villains, just like her father…