The Doctor and Fitz, traveling in Compassion, are forced to make a sudden and unexpected landing to avoid the Time Lords, who have picked up their trail again and are still trying to hunt down Compassion to use her for TARDIS breeding stock. They land inside an Edifice made of solid bone, a huge flower shape hanging in the skies over Gallifrey. The three are quickly separated (drink).
The Edifice is eventually revealed to be the TARDIS, presumed destroyed over Avalon, striving desperately to do something about the Doctor's two histories: whether he died on Dust, or Metebelis Three, has great significance. Its collapse ultimately destroys Gallifrey, which is rapidly falling to Faction Paradox.
The Ancestor Cell provides examples of:
- Back from the Dead: The TARDIS.
- Body Horror: Ryssal is hit with a time-distortion weapon and forcibly regenerated multiple times before being shot to death.
- Bring My Brown Pants: Compassion seriously malfunctions, crashlands in a horrible spooky place, and spits out everything inside her, including the Doctor and Fitz, who admits to farting with terror:The Doctor: "[...]There's a stench of decay here."
"Sorry." Fitz smiled and wafted with his hands. "That would be me. Well, I was very frightened." - Determinator: The TARDIS held on through her own destruction in order to keep protecting the Doctor's real timeline.
- The End of the World as We Know It: Gallifrey is caught in the collapse of the Edifice and destroyed.
- Evil Versus Evil: Faction Paradox vs. The Time Lords.
- Face–Heel Turn: Romana, kind of.
- Future Me Scares Me: Grandfather Paradox is a manifestation of the Eighth Doctor who was consumed by the Paradox biodata virus, and the TARDIS is the only reason that version of the Doctor isn't already a certainty.
- Götterdämmerung: Both the Time Lords and Faction Paradox are virtually annihilated - the Time Lords by the collapse of the Edifice, and the Faction by the destruction of the Eleven-Day Empire. Both sides are, in their own way, gods.
- Love Makes You Crazy: Father Kreiner just wanted the Doctor to come back for him.
- Love Makes You Evil: Father Kreiner again.
- Make Wrong What Once Went Right: Faction Paradox declare all-out war on Gallifreyan history and win.
- Mirroring Factions: The Time Lords are engaged in the same kind of paradox abuse as The Enemy will get up to, building weapons they haven't invented yet based on information from the future. When the Doctor calls Romana out on this, she points out that his Faction biodata infestation means that he's fast becoming the expert on it.
- Myth Arc: This book culminates the Faction Paradox arc that stretched all the way back to Alien Bodies
- Retcon: Romana is now a Evil Overlord while the much-less-beloved but still lovable anarchist Faction Paradox is re-envisioned as psychopaths.
- Retgone: Gallifrey's destruction means it never was, which makes no damn sense given their responsibility for damn near everything in the universe's distant past.
- Ripple-Effect-Proof Memory: Fitz proves impervious to the Faction's attack on Gallifrey's history, noticing the perpetually shifting number of founders.
- Running Gag: "No, these shoes fit perfectly."
- Set Right What Once Went Wrong: The TARDIS has almost allowed its entire existence to be twisted around trying to preserve the timeline that existed before the Third Doctor's alternate regeneration on Dust, giving the Doctor a chance to put things back the way they should be and escape his infection with the Paradox biodata virus.
- Spirit Advisor: As part of the Edifice's nature, it manifests a "ghost" of the Third Doctor from the dust in the console room, which appears to be essentially a manifestation of the part of the Third Doctor's timeline that ceased to exist when he regenerated ahead of schedule.
- Take a Third Option: During the confrontation with the Doctor and the Grandfather, the dust-ghost of the Third Doctor observes that the Doctor has three options; leave the fight for Gallifrey and give up, try to beg the Grandfather for mercy, or a third option that he is prevented from sharing when the Grandfather destroys the image. The Doctor concludes that the only option is to drain off the energy holding the Edifice together by firing the ancient weapon systems, forcing the universe to "choose" whether the original reality or the infected timeline will become real.
- Trauma-Induced Amnesia: The Doctor destroys Gallifrey (for the first time) and both the psychological and temporal after effects leave him unable to remember anything about himself.
- The Virus: The Faction's incidental biodata attack on the Doctor is starting to bear fruit.
- Wham Episode: Gallifrey is destroyed, the Doctor's memory lost, but at least his biodata infection is presumed cured. On the bright side, the TARDIS is back.
- Where I Was Born and Razed: For the first time.
