The book opens with four-year-old Kate being hastily awoken by her mother and told that she must take care of her siblings. The three children are then hurried away with three unnatural men in chase, and left in an orphanage.

Years later, Kate, Michael, and Emma P are unhappily ensconced in the last of a succession of orphanages, and after talking back to an awful prospective parent they are sent away to a new orphanage at Cambridge Falls. Cambridge Falls is quite mysterious; no one seems to know about it, except the man Abraham who arrives to ferry them across the water to it, and when they arrive the town appear to be almost wholly dead, and they are surprised to find it abutting a mountain that they hadn’t noticed before.

They are hurried to the house by Abraham where they meet Miss Sallow, a rude and unhappy house-keeper who informs them they are the only orphans living there. When Abraham leads them to their rooms, he gives them a photograph of a lake and tells them that there used to be a dam.

When they explore the house the next day, they discover a room in the basement with a brilliant green book sitting in it. Michael, ever the historian, takes a photo with his polaroid. They discover the book is completely blank, and saying that it would make a good scrapbook, Michael lays the photo Abraham gave them in the book.

They find themselves instantly transported to the location in the photo, surprising a much younger Abraham. Before they can figure out what is going on, there is a terrible screech and a decomposing monster of a man lopes out of the woods and collects the three children. They are herded into a group of many other children who are being forcibly kept separate from their parents by more of the creatures, which Kate learns are called Screechers.

Before they can escape using the photograph that Michael took back in their own time, they are interrupted by the Countess of Cambridge and her odd-looking secretary Mr. Cavendish, who tells the mothers and children that she is sick of waiting for their menfolk to find the thing she needs and that she will throw a child off the dam for every day they fail to find it.

A giant man runs out of the woods and attacks the Screechers, but is overpowered.

Kate, Michael, and Emma at this point make good their escape using the Atlas, but when they arrive back in the basement room Kate and Emma discover that Michael somehow managed to be left behind.

Kate is disturbed when she handles the book because it causes visions, and she sees blackness seep out of the pages and into her fingers.

When Kate and Emma go looking for Abraham to get a new photograph the next day they learn he has gone to pick up their guardian, Dr. Pym. Unfortunately, they are corralled by the doctor before they can get ahold of Abraham, and they find themselves telling him their entire life story (thanks to the magical book, they suspect him of being a wizard). Afterward he recommends they ask to see the last photograph Abraham ever took.

They track down Abraham and he gives them his whole collection of photos, including the last one he ever took. However, although he admits he remembers them, he refuses to tell them anything of substance about the past. On sifting through the collection they find a photo of Michael holding a sign that reads “Help”. They use this to go back, but are surprised by the Countess’ secretary and a bunch of Screechers. Michael, it turns out, has betrayed them.

They are taken to the Countess, who explains that the book is what she has been looking for. However, this copy is no good for her because two copies of the same thing cannot exist at the same time and the book fades away before their eyes. They also discover that Michael sold them out because the Countess promised to help find their parents, but she of course lied. She also tells them her creatures are technically called morum cadi All three children are thrown in with the other orphans.

The young Abraham shows up just as Michael is about to be strung up by the other orphans for being a traitor (although Emma and Kate eventually forgive him), and he shepherds them out through a secret passage. On their way, they overhear the Countess talking to her secretary about her master, and how she will likely keep the book for herself when she finally finds it. She also mentions that she noticed that Kate had been marked by the book.

The three make it out of the house, but the Countess discovers they are gone and sends her mostly-starved wolves after the children. Fleeing the wolves, the children are chased down a cliff face, and eventually cornered by three wolves only to be saved by the giant who had attacked the Screechers, who has evidently just escaped the Countess, as well. He tells them his name is Gabriel, and leads them through the forest to a cabin where they can rest.

Emma finds herself strangely drawn to Gabriel, and before her siblings wake up follows him out in the wood and witnesses him kill a deer. When everyone is up, Gabriel reveals that Cambridge Falls is part of the magical world, which has been pulling further and further away from the mundane world for years. He escaped from the Countess’ boat, which is home to some unknown monster. Michael hypothesizes that the Countess keeps the creature on the boat because it is hydrophobic.

Finally, Gabriel tells them he is going to his village to warn them about the Screechers, and that they should stay at the cabin. However, they are interrupted by a pack of Screechers that have tracked them, and all four are forced to flee into the mountain.

The Screechers finally catch up to them at a bridge across a chasm. Gabriel tells the children to go ahead while he tries to delay the Screechers, and they rush off.

In the maze beyond the bridge, however, Kate is overcome with a vision, and she plunges into the maze. Michael follows her, but Emma turns back to help Gabriel.

Michael and Kate make it through the maze to a dead-end, where they are ambushed and taken hostage by dwarves. The dwarf captain Robbie McLaur imprisons them based on orders from King Hamish, and sticks them in cell 47 which turns out to contain Dr. Stanislaus Pym. Kate and Michael tell Dr. Pym what has been happening, and beg him to find Emma. He reveals that he cannot do much magic in the dungeon thanks to dwarven iron, but that Emma was wounded saving Gabriel and taken to his village to be healed by the wisewoman Granny Peet.

Kate, Michael, and Dr. Pym are taken before the dwarf king, who has entered into an agreement with the Countess to let her force the townsfolk of Cambridge Falls to dig in the old dwarf capitol, the Dead City. He has evidently been eavesdropping, because he knows about the book and wants it for himself. Dr. Pym reveals that only he or one of the children can open the vault the book is stored in, and convinces Hamish to take both Kate and Michael with him. Michael calls out Hamish for his un-dwarfish behavior.

Meanwhile, Emma is healed by Granny Peet, helps heal Gabriel, and then helps convince the tribe elders that they must fight the Countess or face the death that she knows will subsume the area in the future she comes from.

Kate, Michael, and the Dwarves (including Wallace, a dwarf sent by Robbie to protect them) make it to the book, and Kate convinces Hamish that she must be the first to touch the book on orders of Dr. Pym. When she does, she is whisked even further into the past to Dr. Pym’s study. There he takes the book, and she briefly sees her mother before being pulled back to the present sans book.

The dwarves and children are captured by Screechers and the secretary as they emerge from the book’s vault. Michael and the dwarves are imprisoned with the rest of the Cambridge Falls townfolk while the secretary talks to Kate alone. He tells her that the book is just one of three Books of Beginning (which contain the power to create or recreate the universe), and is called the Atlas of Time. He also coerces her into telling about going into the past, and realizes that Dr. Pym has cleverly hidden the book in the past where the Countess cannot get it.

They are interrupted by Gabriel’s attack, however. Kate manages to free the dwarves and townfolk, turing the battle to the advantage of the townsfolk until a wave of salmac tar, who the Countess has also been entering into agreements with, comes up out of the depths. Things are looking grim, but Robbie McLaur comes out of nowhere with an army of dwarves and saves the day. It turns out that with Dr. Pym’s help he found the previous ruler’s will, that named Robbie the king instead of his older brother Hamish.

The dwarves, townsfolk, and tribesmen are planning on attacking the Countess, but Kate sees a vision that convinces her the Countess will destroy the dam and take the children with her into death rather than face failure and her master. Kate sneaks out, frees the secretary, and with his help is transported to the Countess to bargain the book for the children’s lives with everyone else hot on her heels.

Dr. Pym uses magic to get a small group to the town very quickly, and Gabriel and Emma head to the dam to defuse the mines that the Countess has placed, while Michael and Dr. Pym grab a boat and go to rescue the children.

Meanwhile, Kate has gone back into the past with the Countess’ help, where she talks with her mother (and is comforted by her), and then returns with the book. Once the Countess has the book, she refuses to help the children, but they are interrupted by Dr. Pym. Meanwhile, Michael is helping ferry children to shore.

The Countess traps Dr. Pym, but he magically calls her master, the Dire Magnus, who inhabits the Countess’ body, unnaturally aging it. The Magnus tells Kate that she is tied to the Atlas and her siblings and she are fated to find the other books and then join him or some such. He departs before the Countess’ body completely destroys itself, and Dr. Pym is left unconscious. Kate drags him out on the deck of the boat to find the children in chaos.

Back in the dam, Gabriel is forced to fight the Countess’ monster while Emma disarms all of the mines but one. Gabriel is knocked unconscious by the monster, and Emma saves him by shoving him to a lower catwalk just before the mine explodes right next to the monster. She is able to wake up Gabriel and they try to make their escape, but the monster has survived and almost beats them to the door. Gabriel grapples with the thing, and they fall into the depths of the dam as Emma escapes.

Michael finds Emma on top of the dam, and before she can stop him, jumps down to the boat as it passes beneath them on the way to the falls. Michael shows Kate that he has the last photo Abraham ever took, and they use it to escape death. Oddly, doing so does not consume the photo as it always has before, and Dr. Pym says that it is because Kate is coming into the power of the Atlas.

The children return to the present, and Kate goes to hide the atlas while her siblings follow Miss Sallow down to dinner. She is interrupted by the aging Countess, who was not killed by the Dire Magnus after all but succeeded in latching onto the line of children and was thus saved from death. She has been waiting for fifteen years for Kate to return, and has come to claim the book. Without using a picture, Kate transports them both to the ancient city of Rhakotis where the Books of Beginning were originally created. The Countess reveals that the three children are tied to the Books of Beginning through prophecy, and that their parents are prisoners of the Dire Magnus in an attempt to get Kate not to leave her behind, but Kate abandons the Countess as the city burns around them.

The children go to Christmas Eve dinner, where they discover the children they saved, now fifteen years older but entirely grateful. They are happy to discover that Gabriel also survived by drowning the monster, and then swimming to safety. Although Kate knows that they must eventually go free her parents, she finally relaxes with her siblings.