Apparently, when the Great Houses sealed Cousin Justine into her own past, it didn’t occur to them that her Faction training would enable her to change that past so she could deliver a warning to her future self, or that she could then use the shadow of Grandfather Paradox to create a shadow weapon capable of cutting through the time-frames and freeing her from her casket. This has made Demetra Kein’s mission more complicated, but she was prepared for such an eventuality. On her orders, Selvynkesh releases four specific inmates, soldiers from the Blood Coteries with time-active protocols tattooed directly into their biodata. They are effectively hunting dogs primed to track down Faction agents through history, but they’re also very obviously marked with the secrets of the Great Houses, which is why they ended up here. When Selvynkesh learns that the forces now approaching the prison are not the House Military, but the Blood Coteries, he realises that Kein had herself and the tattooed soldiers placed here deliberately. The Coteries have a vendetta against the Cousin who carries Grandfather Paradox’s shadow, they knew the Cousin in question would eventually end up here, and they knew that one day a prison break was inevitable; thus, Kein deliberately experimented with time travel in order to attract the Great Houses’ attention and get herself here, all to capture the Cousin and take her back to Siloportem.
In the labyrinth, Justine and Shuncucker fight each other to a standstill as Veeble vainly tries to remind them that they’re on the same side. Once things have calmed down, Justine notices that Shuncucker seems oddly familiar. Shuncucker grandly introduces herself as the last scion of the Faction homeworld, and insists on staying to fight Kein, whoever she is. Seeking a way out of the labyrinth, they find themselves in a library full of the Great Houses’ secrets, printed out in hard-copy and stored outside of normal time to escape any changes to history. They are then set upon by Kein’s tattooed hunters, who prove immune to shadow weaponry. Shuncucker thus grows a shadow flamethrower and sets fire to the library shelves, driving the creatures back. Veeble and Justine flee, but Shuncucker stays to fight the creatures.
Justine is separated from Veeble and encounters Mr Smith, a polite bull-headed man in a waistcoat. Mr Smith identifies himself as a function of the library rather than a living creature, and convinces Justine that trying to attack him is pointless. He then informs her that she is mentioned in some of these books, particularly the chapterhouse records of House Lolita -- and in a text written by Godfather Morlock. Mr Smith shows her the book in question, and when she turns its pages, she seems to be transported back to the day the Faction hunters attacked Fiora’s cottage...
Young Justine awakens from her fit, but is haunted by the feeling that something important is taking place a long way away. Outside the cottage, she hears Godfathers Sabbath and Morlock discussing the hunt; strange as it seems, Sabbath apparently intends to kill Fiora because she’s his great-grandmother. Morlock, however, has taken an interest in the temporal distortion they noticed earlier, and makes a wager with Sabbath; if he should fail to take his target, then he must allow Morlock to take one of the two girls as a protégé, even though Morlock’s last experimental subject was driven mad.
Justine tries to warn Fiora and Emma of the danger, but they don’t take her seriously until the hunters break into the cottage with their shadow weapons. As Sabbath prepares to take Fiora’s life and Emma begs for mercy, Justine tries to understand what’s going on. Morlock explains that Sabbath has been appointed the head of Faction Paradox’s military wing, and he’s killing his own ancestors, working his way backwards through the family tree, so that he is no longer rooted to history and thus no longer vulnerable to attack. However, there are specific rules to the ritual, and Justine asks Morlock to find a way under these rules to save Fiora’s life. Morlock therefore informs Sabbath that Fiora is already pregnant with Sabbath’s grandfather; the rumours about her and Mr Faraday were true. The rules state that he can’t kill the same ancestor twice, and Sabbath has therefore missed his chance to kill Fiora. When he learns that Emma is Fiora’s closest relative, however, he strikes her down instead, hoping that her death will open a few more windows of possibility that will enable him to continue the hunt.
The horrified Justine vows not to let Morlock and Sabbath get away with her friend’s murder, but Morlock points out that she is hardly qualified to fight monsters... unless she agrees to let him teach her. She still sees human life as sacrosanct, but his people see the wider picture; their vision encompasses history and culture, they know that the physical self is irrelevant when compared to the patterns they leave and the stories they tell, and their weapons are made of culture and history. Some part of Justine understands what he means by this, and Morlock departs, knowing that one day they will meet again.
In the labyrinth, Justine drops the book, knowing that she’s been given an important message. Mr Smith shows her the way out of the labyrinth to the outrigger platform, which Shuncucker and Veeble have already reached. Veeble is reunited with Selvynkesh, who admits that he’s responsible for this chaos, though he can no longer remember why it seemed like such a good idea. Shuncucker storms onto the platform to confront Kein, who recognises her at once; Shuncucker is the one who wronged the Blood Coteries, stumbling through Siloportem and crippling their thousand-year-old empire. Since their last meeting, Kein has re-engineered her biodata to ensure that shadow weapons have no effect on her. The faceless hunters then arrive, but before they can attack Shuncucker, Justine arrives, armed with the knowledge she acquired from her memories. This war is about weapons that can rewrite history -- and the faceless hunters are immune only to the physical effects of shadow weapons. Before Kein can stop her, Shuncucker grows a memetic pick from her shadow and rewrites the hunters’ biodata tattoos. She then sets the hunters on Kein, and they tear her apart and throw Mendeema over the side of the platform, out into the ever-changing depths of history.
Justine realises that Shuncucker can’t be reasoned with; she saw her people slaughtered, and all she can do now is kill in return. Justine leaves her and the hunters to face the incoming Blood Coterie ships while she retreats to the prison proper. The House Military has arrived in force, and the panicking inmates have released more prisoners -- who don’t know what they’re doing here and are just shooting everything that moves. In the confusion, Selvynkesh suddenly addresses Justine directly, and Justine realises that he’s channelling the spirit of Mistress Mary Culver. Justine’s friends couldn’t rescue her while the Great Houses were watching, and Mistress Culver thus influenced Selvynkesh to create chaos within the prison. Now, the House Military has opened up so many channels that the rescue timeship can slip in and out without being noticed.
Before releasing Selvynkesh, Mistress Culver advises Veeble to avoid the current unpleasantness by entering a casket and waiting for the House Military to sort out who’s who. Justine then returns to Earth, where she is reunited with Cousin Eliza. A lot has changed since Justine’s trial, but before dealing with the new situation, Justine visits Geddis Fields to remember her late cousin Emma and the face she once saw in the sky. She is starting to wonder what Morlock was really up to, and fears that the burden of the Grandfather’s shadow is driving her mad.