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An infected version of the Doctor's personal timeline was created when Faction Paradox infected the Third Doctor with a biodata virus. In this version of history, the Third Doctor died of a gunshot wound incurred on the planet Dust instead of radiation poisoning while fighting the Eight Legs. (PROSE: Interference) By one account, this timeline resulted in the paradoxical origins of both the Enemy and Faction Paradox, making it coterminous with the War in Heaven timeline as a whole. (PROSE: The Ancestor Cell)
The Edifice, a half-dead future version of the Doctor's TARDIS, contained the paradox, holding both timelines in superposition and allowing the Doctor's life beyond their third incarnation to remain mostly stable. Things finally came to a head with the Doctor forcing a choice between the two versions of his life, purging himself of the biodata virus, restoring the Third Doctor's original death, and averting the War in Heaven. (PROSE: The Ancestor Cell)