In the year 6012, the ship was sent to establish a colony on Messaline with humans and Hath. However, shortly after arrival, the mission commander died of Byzantine Fever and war broke out between the humans and the Hath who abandoned their ship.
During the war that followed, in which the progenation machines resulted in hundreds of generations of humans and Hath per day, the ship's true nature became forgotten and it was known as a holy temple instead where a mythical weapon known as The Source was located. After the arrival of the Tenth Doctor, the ship was rediscovered by the Doctor and his companions Martha Jones and Donna Noble. The three were originally surprised to find the ship still had power, but pieced together the truth of the war after the Doctor read the mission log and Donna realised that only a week had actually passed since the start of the war, not hundreds of years. After finding the Source, a terraforming device, in the ship's greenhouse, the Doctor ended the war by releasing the terraforming gasses and proving to both sides the truth of their mission.
Following the murder of Jenny by General Cobb, her body was placed in a room on the ship for her sacrifice to be honoured. Suddenly, Jenny returned to life, either due to a partial regeneration from her Time Lord genetics or due to the effects of the Source. Jenny then stole one of the Temple's shuttles and took off into space to follow in her father's footsteps. (TV: The Doctor's Daughter)