The Doctor was a renegade member of House Lungbarrow, the tenant of an outdated renegade timeship christened "the TARDIS." He died on Dronid during the first battle of the War. He had unique biodata, which made his body, the Relic, a potential weapon to the War-time powers.
Biography
Needs information on Interference.
In his third incarnation, accompanied by Sarah Jane Smith, he was summoned by his future self to Dust, where his timeline was radically altered due to him dying before he was supposed to. (PROSE: Interference - Book One, Interference - Book Two)
For a time, the TARDIS was also occupied by two 30th century Adjudicators, Roz Forrester and Chris Cwej. (PROSE: Original Sin) Forrester died (PROSE: So Vile a Sin), and Cwej joined the House Military. He received briefings (PROSE: The Book of the War), making him remember the Doctor as the self-title "Evil Renegade" who kidnapped them and murdered Forrester. (PROSE: Dead Romance) Helen Greyridge had her memories altered in a similar fashion. (PROSE: Judy's War)
The Doctor met Carmen Yeh on a shipping vessel where ElleryCorp was using her as a test subject for their human isolation experiments; he then saved her from the murderous onboard artificial intelligence. (PROSE: Schrödinger's Botanist) After many travels together, the Doctor accidentally left Yeh in Alaska 1758. (PROSE: Carmen Yeh)
Along with Samantha Jones and representatives of the various War-time powers, the Doctor attended the auction of his body in the East Indies, ReVit Zone late in the 21st century (PROSE: Alien Bodies)
In 2002 San Francisco, the Doctor and a version of Sam encountered a little boy from Faction Paradox. (PROSE: Unnatural History)
The War indirectly intersected the Doctor's life again when he encountered the Remote on Earth in 1996. One of them, Compassion, took up residence in the TARDIS. (PROSE: Interference - Book One, Interference - Book Two)
After the TARDIS was destroyed and Compassion became a timeship, the Doctor moved into her. He was with her as she went on the run from the Homeworld. (PROSE: The Shadows of Avalon) He forced a randomiser onto her, hoping that it would make their movements less predictable. He travelled with her to Yquatine (PROSE: The Fall of Yquatine), Eskon, (PROSE: Coldheart) and Banquo Manor, where they were finally caught by Cuthbert Simpson, who had obtained the randomiser's seed code. (PROSE: The Banquo Legacy)
The Doctor was taken with Compassion to the Gallifrey where Romana was War Queen. It was invaded by War-era Faction agents, and the Doctor destroyed the planet to end the War before it had begun. (PROSE: The Ancestor Cell)
While on Earth in the 18th century, the Doctor's heart — which linked him to a Homeworld which had never existed, poisoning him — was removed by Sabbath. Ostensibly this was to save the Doctor's life, but when Sabbath planted it in himself he gained the ability to travel through time. (PROSE: The Adventuress of Henrietta Street)
After dying on Dronid in the first battle of the War, the Doctor's body (known as the Relic) went missing. When it was discovered by the Corporation, hidden in a bunker under the city center, Celestis agents worked with Little Brother Kolman to steal it for Faction Paradox; however, Cousin Sanjira didn't recognize its importance and instructed Little Sister Justine to dematerialize it. From there, it ended up in the Americans' "Toy Store", which was pillaged when the Daleks invaded. By 2169, the Black Man had it in his store in London, though he sold it to Qixotl shortly before Homonculette came looking for it. (PROSE: Alien Bodies)
A future version of the Eighth Doctor, infected with the Faction biodata virus, was made into a surrogate Grandfather Paradox by the Faction, and, believing himself to be the actual Grandfather, led them in an assault on Gallifrey. (PROSE: The Ancestor Cell)