Doctor Who: The Ancestor Cell(2001)

Trevor BaxendaleStephen ColePeter Anghelides

The Doctor's not the man he was. But what has he become? An old enemy -- Faction Paradox, a cult of time-travelling voodoo terrorists -- is finally making him one of its own. These rebels have a mission for him, one that will deliver him into the hands of his own people, who have decreed that he must die. Except now, it seems, the Time Lords have a mission for him too...A gargantuan structure, hewn from solid bone, has appeared in the skies over Gallifrey. Its origins and purpose are unknown, but its powers threaten to tear apart the web of time and the universe with it. Only the doctor can get inside... but soon he will learn that nothing is safe and nothing is sacred.

Shot by both sides, confronted by past sins and future crimes, the Doctor finds himself a prisoner of his own actions.