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.
- Cloning Blues: Poor Fitz
- 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.
- Face-Heel Turn: Romana, kind of.
- 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.
- Myth Arc: This book culminates the Faction Paradox arc that stretched all the way back to Alien Bodies
- Not So Different: 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.
- 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."
- 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.