The sequel to The Emerald Atlas picks up nine months later with Kate, Michael, and Emma back in their rather disagreeable Baltimore orphanage where Dr. Pym leaves them after mysteriously leaving on Christmas Eve. When monsters interrupt the uppity orphanage director’s party, the trio make their hasty exit through time and space. Or rather, Michael and Emma make an exit for Dr. Pym and Kate drags the beast one hundred years into the past.
Their stories are told in linear fashion with Michael and Emma searching for the second of the Books of Beginning, the Fire Chronicle. The two take on their beasts, the Dire Magnus’ legion of Screechers, and Michael and his cunning use of logic becomes the Keeper of the Fire Chronicle. But before he can grab hold of the Chronicle, the two meet up with Gabriel and head to Antarctica. They meet the Guardian who protects the Chronicle until its Keeper arrives. The problem of course is that the Guardian has been protecting the Chronicle for thousands of years and is unlikely to give it up anytime soon. Also, its doubly protected by an elf princess who has been turned into a dragon. Also, its in the bottom of a volcano.
Meanwhile, Kate is one hundred years in the past where the Separation has yet to occur. The magic world and non-magic world are entwined but not for long. Magic folk have been hunted and killed forcing them into hiding. The magic world will soon disappear (at least from view of the non-magic folk). Kate joins up with a group of orphans all possessing some magical ability including their young leader, Rafe. Rafe and Kate know each other somehow but so does the Dire Magnus. He is prepared to rip not only the two apart, but the entire world to maintain his power, his influence.