Months after the end of the first book, Kate, Michael, and Emma are back at their old orphanage. Dr. Pym sent them back a mere week after they survived their first adventure because he and Gabriel had to run off to deal with some unnamed threat. Kate is nervous, however, because she has been having dreams about a mysterious and powerful man tracking them down by visiting their previous orphanages.

It turns our her dreams were correct, and the orphanage is attacked by Screechers. The children end up in the headmistress’ office, and are just about to escape using the atlas when Kate is grabbed by a Screecher. She has Michael promise to look after Emma, and uses the Atlas to transport herself into the past. Michael and Emma are summarily saved by Dr. Pym emerging from a wardrobe and dragging them back through it to Italy.

It turns out that Dr. Pym’s wizard friends have been getting themselves killed by the head henchman of the Dire Magnus, a giant bald man named Rourke. He has brought the children to Italy to visit another of his past colleagues. The man hears his warning, but refuses to help out, and tells the story of how the children’s parents came and visited him shortly after giving up their children to Dr. Pym. Apparently they had heard of the trail for one of the two remaining Books of Beginning was in a South American town called Malpesa (a magic town that’s off the map, similar to Cambridge Falls). Sadly, Rourke tracked down the man and forced him to tell him where the children’s parents were headed, so the Dire Magnus was able to capture them.

Dr. Pym, Michael, and Emma head to Malpesa and troupe through the graveyard where they easily happen upon the grave of the man who was heard to mention the books of beginning two hundred years ago. Michael gets past a cave in and solves a riddle that allows him to inherit the previous keeper’s memories of the location of the book (which is called the chronicle of life). The three barely escape the graveyard ahead of Rourke and a bunch of Screechers.

They flee through town, and when they are foiled at getting to the port and saftey, they climb a tall building and Dr. Pym sends a signal up in the air. He stays behind to delay Rourke, and tosses the two children into the bay where they are picked up by a plane with Gabriel on board.

At Michael’s instruction, they fly to Antarctica, and after picking up supplies at a handy outpost on the way head to a pair of mountains where Michael leads them through a snow storm to a tropical valley that houses a volcano and the chronicle (the tropic paradise having been created by the chronicle, since it causes life to thrive around it).

Meanwhile, Kate is back about a hundred years in time in the year 1899 in New York City. She was barely able to rid herself of the Screecher by hopping through several places and times, and when she got to New York passed out for a couple of hours, causing the atlas to fade away (since it can’t exist in the same time twice). She is found by a pair of ragamuffins who try to take her to see a boy named Rafe, but she gets it into her head that she needs to set off on her own and ignores their advice not to talk to a witch in the magic quarter (it turns out that this is just before the Separation, which caused the mundane world to forget the magical one). The witch drugs her and sells her to a gang called the Imps, but she is saved by Rafe himself. Oddly, Rafe apparently knows her even though they have never met before.

He leads her back to his gang’s hideout, where she meets a crazy old wizard who hides the church the gang lives in, and the witch who runs things. She also gets to know some of the children in the gang. Unbeknownst to Kate, Rafe goes to visit a seer to learn about her, and we discover that he knew her from a dream in which she told him his destiny and then died. The seer confirms this will happen. We also learn that someone is hunting for Rafe, and the adults in his gang are trying to protect him.

Kate and some of the other children go out on a shopping excursion. While they are out, she has some alone time with Rafe and realizes she likes him a lot. They leave him after eating lunch, however, and the children discover some normal humans heckling some magic users. Although the humans turn aside, two of the children throw snowballs at them, which transform into colored gunk (thus giving away the fact that they are also magic users). Kate tries to lead the hoodlums astray, and runs up literally running into Rourke, who takes her to the Dire Magnus.

The Dire Magnus is an extremely old man, who tells Kate that not only will the Separation be happening that night, but that he will also be dying. Apparently the Dire Magnus dies every so often and passes his combined memories into a new body. In this case, they are looking for Rafe and planning to catch him when he comes to save Kate. Rafe outwits them using a glamour that makes him look like Rourke, however, and the two escape.

They return to the church hideout to discover it burning. Rafe is largely immune to fire, so he is able to get most of the children out, but Kate follows him in when he goes to save the witch in the top of the church. Once they get up there, the witch reveals to Kate that she knows that Rafe is destined to become the newest Dire Magnus, and tells Kate that the only way to save him is to “love him as he already loves her.” She is also already dying and past saving.

Once Kate and Rafe escape the church, Kate urges Rafe to come away with her, and when he asks reveals the truth about why the Dire Magnus wants him. He seems tempted, but then one of the hoodlums from early shows up with a gun and shoots Kate.

Rafe takes her to the Dire Magnus and makes a bargain: if the Magnus saves Kate by sending her back to her brother and the chronicle (which can presumably save her life), then he will become the next Magnus. The Magnus assents, and triggers Kate’s gift.

While all that is happening, crazy stuff is going on back in the jungle of Antarctica. Michael and Emma witness some very vain elves dancing and singing around an ice sculpture with a crown, which Michael takes. Emma is then grabbed by a dragon and spirited away with Gabriel and Michael in hot pursuit.

They arrive at the volcano to find Emma frozen by a magical poison and the last remaining guardian, who is mad, tells them that the keeper of the chronicle will need to go order the dragon to fetch the book for him. Michael heads to the heart of the volcano, where he discovers that the guardian lied to him; the guardian had transformed an elf princess into the dragon, and she is slaved to his will. He wants her to kill Michael. Michael is able to bargain that she show him the chronicle before killing him in exchange for the golden elf princess crown, and he runs to the exit where the guardian taunts him until Gabriel sneaks up behind him and clocks him over the head. The two flee to the tower where Emma is stuck, and the dragon tears off the top of it, shows the chronicle to Michael, and tells him that because he has shown such spirit he can stab her once before she kills him. He stabs through the gold bracelet on the dragon, transforming her back into the elf princess, they tie up the mad guardian, and he uses the chronicle to heal Emma. Unfortunately, a side effect of the healing is that Michael has to live through the life of the person he is healing, which he finds impossibly difficult to handle.

The elf princess, whose name is Wilamena, has decided that Michael and she will be marrying because he saved her. She sends a signal to her fellow elves to come and fetch them.

Unfortunately, Rourke shows up with an army of Screechers, Imps, and trolls and lays siege just after the elf contingent arrives. He tries to convince the children to give up by parading their father out and threatening to kill him, but Michael figures out that the man isn’t actually their father, and when the elves shoot him they discover Michael is correct; he’s some random guy who was under a glamor. Rourke attacks and things are looking bleak until Michael uses the chronicle to heal the guardian’s madness so that they can reforge the magical bracelet and turn Wilamena back into a dragon. She does some damage, but then is mortally wounded and crashes into the forest.

The guardian prevents Michael from getting killed and is himself slain in the process, but not before telling them there is another way to escape through the volcano. Gabriel, Michael, and Emma flee that way with Rourke hot on their tail. Gabriel stays back to grapple with Rourke while the two children run around the edge of the volcano, which is threatening to explode. On the way, Michael tries to heal Wilamena using the chronicle, but is unsure if it worked. Emma and Michael almost escape, but are intercepted by skeletal Screechers (burned by Wilamena). They end up falling towards the lava at the same time that Rourke and Gabriel go over, but Wilamena swoops in and saves everyone.

Rourke is able to slip away in the ensuing flight somehow, and the rest end up in the elf village where they are reunited with Dr. Pym, who evidently survived his battle with Rourke. Kate has also shown up, but is quite dead and Michael is unable to help her. He also learns that Dr. Pym might not be completely trustworthy; apparently part of the prophecy that involves the children says that when they bring the three books together, the books will combine into one and the children will die.

With Wilamena’s help, Michael travels to a land where spirits can live, and finds a ghostly version of the old church from the past. Inside is Rafe as the Dire Magnus and a dead version of Kate. Michael makes a deal with the Dire Magnus to use the book to resurrect him (his body has evidently been preserved in the real world by his followers, even though he was banished to the spirit realm by Dr. Pym) if he will release his hold on Kate and allow Michael to heal her, as well. The Magnus agrees, but interrupts Michael partway through his own healing and breaks the stylus that Michael has to use to write the name of the person he wants to save. The Magnus tells him he has some things he wants to do before the children are able to interfere, but that he will release Kate in time.

Michael realizes that he doesn’t need the stylus to access the full potential of the chronicle, however, and after the Magnus leaves is able to revive Kate anyway.

They return to the elf colony to find Emma missing. She went off with Gabriel looking for Michael, but it turned out not to be Gabriel; it was Rourke in a glamor, and he abducts her through his portal, leaving her brother and sister frantic behind him.