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The Edifice was the name given to the Doctor's TARDIS after it restored itself following its apparent destruction in a dimensional tear. (EDA: The Shadows of Avalon) Following the Third Doctor's alternate regeneration on the planet Dust (EDA: Interference - Book Two), the TARDIS, sensing that something was wrong, became aware that the Doctor had been infected with the Faction Paradox biodata virus, intended to corrupt him into a member of the Faction. To protect the Doctor, the TARDIS took the virus into itself, holding it in check even as the power requirements for doing so increased to the point where, following its near-destruction, it was forced to draw power from a universe-in-a-bottle created by I.M. Foreman.
Following its destruction, the TARDIS spent around five thousand years drifting in the Vortex before it reformed above Gallifrey, now in the shape of a vast Gallifreyan flower of remembrance - a symbol of death - composed entirely of bone, its interior dimensions mapped onto its exterior making it the same size inside and outside. This also caused it to become a nexus point, affecting past and future events along the causal pathways, generating temporal anomalies in the resulting temporal pulses. Its interior was filled with bone spiders- a relic of the true timeline that it was trying to preserve and restore (DW: Planet of the Spiders)- as well as the temporal 'ghost' of the Third Doctor that should have existed before the Faction's interference, this avatar allowing the Eighth Doctor to realise what had been done to him.
Following the removal of its dimensional stabilizer by the Doctor, he proceeded to drain the Edifice's power by firing its ancient weapon systems, causing its dimensional interface to collapse. The resulting power release destroyed Gallifrey, but also erased the Faction from history as the Doctor forced the universe to 'choose' whether the timeline where he regenerated on Dust or Metebelis III was the 'true' regeneration. As a result of the power loss, the Edifice collapsed down into a small cube, which Compassion and Fitz left in the Doctor's pocket to regenerate while he stayed on Earth, the ship regaining its usual police-box appearance by 2001. (EDA: The Ancestor Cell; The Burning; Escape Velocity)