The Doctor's Daughter

Continuing from where "The Poison Sky" left off, the TARDIS kidnaps the Doctor and his companions Donna Noble and Martha Jones; and whisks them away to the planet Messaline, in the midst of a generations-long war between humans and the Hath, fish-like humanoids. Emerging from the TARDIS, Martha reveals that although she wanted to be home, she did miss the adventure. They are then met by armed men working for General Cobb. Cline, the leader of the men, forces the Doctor's hand in a progenation machine, using his DNA to create a soldier — Jenny, the episode's titular character.
Martha is captured by the Hath, and, following an explosion caused by Jenny, the Doctor, Donna, and Jenny are imprisoned by General Cobb because of the Doctor's pacifist attitude. Each of the primary characters learns about the war from its belligerents; the Hath and humans were initially meant to live in a peaceful colony, but were divided over a dispute about "the Source", believed by each side to be the breath of their creator. When the Doctor unwittingly reveals the location of the Source, the two sides race to claim it first. The Doctor, Donna and Jenny escape their prison cell when Jenny distracts Cline by flirting with him and holding him at gunpoint.
The Doctor is initially dismissive of Jenny but becomes closer to her as the episode progresses. Donna is also intrigued by a series of numbered plaques she notices in each room. When they reach the location of the Source, it turns out to be a terraforming device within a colonising spaceship. They discover that the plaques represent the date the building was completed, which was a mere seven days previous; the humans and Hath have bred so many generations through the progenation machines that their own history degraded into myth. The original casus belli was a power vacuum caused by the death of the mission commander.
Meanwhile, Martha has been making her own way to the Source via the surface with a Hath who dies saving her from quicksand; devastated she reunites with the Doctor and Donna near the Source shortly before both armies arrive.
The Doctor declares the war to be over, and releases the terraforming agent; everyone present lays down their weapons, with the exception of Cobb who tries to shoot the Doctor. Jenny steps in the way and takes a bullet to the chest. The Doctor cries as he holds her, lovingly telling Jenny they have many journeys to take as father and daughter. She replies she'd like to do that, and finally passes away. Enraged, the Doctor picks up Cobb's gun and holds him at gunpoint, to the shock of Martha and Donna, but refuses to shoot him. Angrily, the Doctor orders the humans and the Hath to build their society on the basis of 'the man who never would'.
With Jenny to be given a proper burial by Cline and the Hath, the Doctor takes Martha home. Martha says she can't handle the death and devastation any more and warns Donna that life with the Doctor can be dangerous. Donna nevertheless resolves to stay with the Doctor indefinitely. As Donna leaves them to walk on their own, the Doctor rehashes one of his lines from their time together ("We're making a habit of this"), while Martha expresses her sorrow about the Doctor losing Jenny. He remarks that there's always something worth living for before hugging Martha tightly and departing as Martha happily runs inside her home.
Concurrently, on Messaline, Jenny revives. She escapes Messaline, determined to follow in her father's footsteps by resolving disputes and fighting villains (and a whole lot of running).