The Doctor arrives on Messaline with Donna Noble and Martha Jones in the middle of a war between humans and the Hath. The Hath are an amphibious humanoid race who wear masks filled with water so that they can breathe. When they leave the safety of the Tardis, The Doctor is captured and his hand is forced into a progenation machine which uses the Doctor to make a female soldier. The female soldier is named Jenny by Donna
The Doctor is taken to see General Cobb. The Hath launch an attack on Cobb's base and Martha gets separated from the other two. Martha befriends one of the Hath and together they manage to escape to the land above. The planet is a wasteland and is dark. When Martha gets caught in quicksand, the Hath friend sacrifices his life for Martha to help her out.
The Doctor had to deal with the idea of now being a father to Jenny. At the same time of trying to get used to the idea of being a father, he has to try and bring about peace between the humans and the Hath. To do this, he much find the Source which both the Humans and the Hath are fighting over.
When the Doctor reaches the source, he is reunited with Martha. The Source turns out to be a planet terraforming piece of equipment which the Doctor turns on. General Cobb tries to kill the Doctor but Jenny steps in the way and saves the Doctor at the expense of her own life. The Doctor threatens Cobb with his death but holds back.
After Jenny's funeral, the Doctor leaves with his companions in the TARDIS. Unbeknown to the Doctor, Jenny regenerates with the same face and leaves the planet for adventures of her own.
Jenny is played by Georgia Moffet who is the daughter of Peter Davison who played the fifth Doctor. Georgia would later date David Tennant, the actor who played the Doctor in the episode and they would eventually marry.