The Evil Renegade

"The Evil Renegade" was the title used for the Doctor in the Great Houses' brainwashing of his companions during the War in Heaven.

History
The Great Houses were accustomed to indoctrinating members of the lesser species into willing service through "briefings" and other forms of brainwashing, (PROSE: The Book of the War) and many of the Evil Renegade's former travelling companions proved to be particularly adequate agents. (PROSE: Judy's War)

While working for the Houses, Chris Cwej believed he had been kidnapped by an insane renegade Time Lord, a mad scientist and criminal mastermind who called himself "the Evil Renegade" and carried out experiments on Chris and other captives in the laboritories of his timeship. He also sent Chris's friend to be killed in the middle of a war. (PROSE: Dead Romance) In reality, Chris' travels with the Doctor had been voluntary, (PROSE: Original Sin, et al.) and Roz Forrester joined the war against the Doctor's advice. (PROSE: So Vile a Sin)

According to Cwej's memories, "the Evil Renegade" was the title the renegade had chosen for himself. After hearing Chris' story, Christine Summerfield doubted that anyone would call themselves "the Evil Renegade"; she correctly suspected that these memories had been implanted by Chris' superiors to help control him. (PROSE: Dead Romance) Another name used for the same purpose was "the Defector". (PROSE: The V Cwejes)

Helen Greyridge also had memories of "a strange little man with an umbrella, some sort of evil renegade." (PROSE: Judy's War)

Activities
Before or after he travelled with Chris Cwej, the Evil Renegade traveled with his companions into sphinx-space, where he waged a "one-man war" against the Kings of Space. According to Cwej's edited memories, after multiple spaceship battles and the destruction of the Gods' worshippers' cities, the Evil Renegade escaped, leaving his human slaves behind; however, he kept the Gods' bottle universe, which was ultimately confiscated by the Great Houses when they "caught up with him". (PROSE: Dead Romance)

Behind the scenes

 * Despite the common misconception that the title "Evil Renegade" was used for the Doctor throughout the Faction Paradox series, in reality it was only used in the Virgin New Adventures novel Dead Romance and briefly mentioned in the 2015 short story Judy's War, both times specifically in the context of the Doctor's former companions' edited memories.
 * While it's unclear whether Chris Cwej's memories of the Doctor's adventures in sphinx-space from Dead Romance are accurate, other stories described several other "Doctor-shaped holes" in the War in Heaven:
 * The Rivera Manuscript was an account of an unnamed renegade being captured by the Enemy and drugged with praxis by an interrogator and a mysterious entity called simply "One". In one of the fugue states, he found himself at a Great House during the Event; he made friends with a female servant, babbled about scientific jargon, and quickly became leader of the group of survivors. Dialogue with an Enemy interlocutor included the lines, "Remember / Inside the skin of the sun / It's an option / … Always an option / You keep the sun / In a bottle / You want to know what happens if you lose control / Don't you?" (PROSE: The Book of the War)
 * History recorded that the Doctor died on Dronid in a failed diplomatic attempt just before the first battle of the War in Heaven, (PROSE: Alien Bodies, The Book of the War) but Qixotl knew the true story of the Doctor's death was much more complicated. Even after the fighting had begun, the Doctor visited a dying soldier on Simia KK98. (PROSE: Alien Bodies)
 * After the House Military lobotomised three former renegades and harnessed their minds to babels, which then committed horrific atrocities in the Lethean Campaign, an unnamed assassin broke into the timeship housing them, outwitted the guards, and euthanised the renegades. The babels were then destroyed by the Enemy's forces. The Book of the War speculated that the assassin was likely an associate or a rival of the trio. (PROSE: The Book of the War)
 * When asked by a dying soldier on Simia KK98, the Doctor said that he wasn't working for the High Council but may be of the Enemy "depend[ing on] where you stand." (PROSE: Alien Bodies) When asked who the Enemy was, Abschrift replied, "Who indeed." (PROSE: Warlords of Utopia)
 * Later in the War, the Doctor's corpse became a valuable weapon and asset. When representatives of the various Wartime powers assembled to bargain for it at Qixotl's auction, the corpse's powerful psychic field told Joseph Kortez, "We are all of us living inside the bottle, and one day, the bottle will break." (PROSE: Alien Bodies) Christine Summerfield received the same message from a Ouija board. (PROSE: Dead Romance) The Doctor's corpse was subsequently destroyed by the Eighth Doctor on Quiescia with a thermosystron bomb. (PROSE: Alien Bodies)