The Tardis shines as the true hero of Doctor Who, saving the Doctor's timelines, holding the fabric of time and space together and allowing Compassion to evolve. The symbol the Tardis presented as a harbinger of the end, the Flower of Remembrance, is emblazoned on the cover, signifying Death. The Tardis took the initiative to save and maintain the Doctor and time and space itself. The idea of leaving companions and friends behind is a huge thematic thread throughout the Ancestor Cell. The Doctor is attacked on many occasions for having walked away from people he has left behind.
Compassion has finally comes full circle here.
Once cold and analytical and pragmatic, self-interested out of a sense of practicality that verged on the immoral, the Compassion of The Ancestor Cell makes sure the Doctor winds up in the place he loves most. She previously acted arrogant and abrasive because she just didn't care enough about other people to be polite. She was superior to those around her and didn't care if she showed it. She conflicted with the Doctor and saw the Timelord as an end rather than a friend. As the book ends, the Doctor is essentially lost.