Alastair Hunt, a mage, desperately climbs a mountain glacier to get to a cave. The cave is a refuge for mages too old, too young or too sick to fight in the third mage war. The leaders at the Magisterium had assured Alastair that this remote cave would be the safest place for his wife, Sarah, and infant son, Callum. He left them there to fight behind their champion, Verity Torres, as Verity faced the Enemy of Death in battle.
Alastair enters the cave and finds the body of his wife with a dagger in her hand. Nearby, he finds his infant son, Callum. Though the baby’s leg is badly broken, he is the only survivor in the cave. As Alastair takes the blade from Sarah’s lifeless hand, he sees words she carved into the ice: Kill the child.
Callum (Call) Hunt, now 12 years old, lives in a small North Carolina town with his father, Alastair. Call is known as a troublemaker at school, and he and Alastair live without using magic, except for when Call was being bullied. In those moments, he showed signs of having magical ability.
Alastair reluctantly travels with Call to take a mandatory aptitude entrance exam at a school for young mages called the Magisterium. Even though both of Call’s parents attended the Magisterium, Alastair has cautioned Call about the dangers of magic and the school. Alastair tells Call that he must deliberately fail the test so he is denied entrance. Despite Call’s poor performance, he is awarded a position under the tutelage of Master Rufus, Alastair’s former professor.
Alastair is furious and demands that Call be allowed to return home, but Master Rufus reminds Alastair that once a student is chosen, he must attend. The uncontrolled magic that young mages possess is strong enough to cause danger to themselves and the rest of the world. Students are ushered into a bus and taken to the cavernous, underground Magisterium to begin their first, or Iron year. Master Rufus’ other two apprentices, Tamara and Aaron, share a suite of rooms with Call, and attend classes with him.
Aaron is popular with the other apprentices and friendly toward Call. Tamara is focused on her studies, fearful of disappointing her parents or not living up to the high standards they set for her. Master Rufus’ teaching methods are unconventional, challenging and sometimes tedious to Call.
When his new friends take dangerous shortcuts to get their tasks done and are caught, Call takes responsibility, which earns him a visit to Master Rufus’ office. The teacher tells Call that he was picked because he is too powerful to remain untrained, and if he passes his mandatory first year and demonstrates control over his magic, he can leave the Magisterium and never practice magic again.
If Call fails his first year or leaves before the end, his magic will be bound. After the first year, no one can bind his magic. Call agrees to stay at the Magisterium for the first year because he wants to go home and still have magic.
Call gets a letter from his father. Feeling homesick, Call sneaks into Master Rufus’ office to call Alastair. The excitement Call feels is quickly tempered by his father’s grave warnings that it would be best for Call to leave the Magisterium right away, that the danger is too great and that Call doesn’t know what he is.
After the call ends, Call finds another letter from Alastair, this one addressed to Master Rufus, asking the professor to bind Call’s magic before the end of the year. Call is furious. He thinks his father doesn’t believe in his ability to pass the first year. He takes the letter, and on the way back to his room, he overhears professors discussing the growing power of the Enemy of Death.
The Enemy of Death was a student at the Magisterium named Constantine Madden. Constantine and his twin, Jericho, studied under Master Joseph. Mages draw on the elements: earth, air, water, fire and the void. The void is the source of the most powerful and terrible magic of all, chaos magic.
Constantine was a Makar, a mage who could access the void and create chaos magic, with Jericho as his counterweight to balance the dark powers. Constantine and Master Joseph experimented with chaos magic and the void, putting bits of the void into animals, which turned the creatures insane. One of Constantine’s experiments went horribly wrong and killed his brother.
Afterward, Constantine became obsessed with necromancy, using chaos magic to bring back his dead brother. Constantine was unsuccessful, but he managed to push chaos magic into humans, driving out their souls, making them obey him mindlessly. The Magisterium tried to stop him, but he and Master Joseph escaped.
Eventually, Constantine started the third mage war that killed Call’s mother and other mages, including Verity Torres, the last known Makar. Since then, the Magisterium has been searching for another Makar. They want this person to fight Constantine, when the dark mage comes out of hiding.
Master Rufus asks Call, Aaron and Tamara to search a pool in the caves of the Magisterium as one of their assignments. They find a Devoured, a mage who was consumed by the element of magic, leaving it immortal but without any humanity. The creature makes a prediction about the three students, telling them that one will fail, another will die and the third is already dead. Master Rufus arrives and saves the students, but the ominous prediction leaves Call deeply disturbed.
One night, a fellow first year student, Drew, runs away from the Magisterium. The entire school leaves the caves of the Magisterium to search for him in the woods. Chaos-ridden wolves attack the search party, but Aaron, using chaos magic he didn’t know he possessed, destroys them. The professors are overjoyed. They have finally found the Makar that they have been desperately searching for in their fight against Constantine.
Aaron’s status is elevated, and Call volunteers to be Aaron’s counterweight. On the way out of the woods, Call sees a chaos-ridden wolf pup. While the pup has red eyes like other chaos-ridden animals, it behaves normally. Call thinks that though the pup was born to a chaos-ridden mother, its soul is intact.
He sneaks the orphaned pup, Havoc, into the Magisterium and keeps it as a pet. After Aaron and Tamara get over the shock of having a red-eyed animal living in their apartments, they come to love Havoc. They even take turns taking care of him.
Aaron takes Havoc out of the Magisterium for a quick walk. When he doesn’t return, Call and Tamara search for him. They find a frantic Havoc, who leads them to an abandoned building with chaos-ridden elementals and people. The children think Constantine has kidnapped him. But they find their friend tied and dangling from the rafters above a tank of chaos-ridden elementals and are shocked to see Drew guarding him.
Call distracts Drew while Tamara climbs up to free Aaron. Drew pretended to be a naïve Iron year student, but he has been working for the enemy. He pretended to run away from the Magisterium so he could contact his master. Drew unleashes a chaos-ridden elemental beast on Call, while Tamara frees Aaron. Call and Havoc fight the elemental until the wolf is seriously hurt and Call grows angry. The elemental shrinks back from Call. It attacks Drew instead.
Running from the elemental, Call takes Havoc and escapes in a different direction from Tamara and Aaron. A man in a silver mask saves him. Call recognizes the mask as the one worn by Constantine, the Enemy of Death.
When the man finds that an elemental killed Drew, he is grief-stricken and angry. Instead of attacking Call, though, he bows to him. The man is Constantine’s old professor, Master Joseph. Drew was Joseph’s son.
Master Joseph and Drew used Aaron as bait to draw Call to them. He tells Call that he is Constantine. Constantine was greatly injured in the mage war. When he felt himself dying, he used what he knew about moving a soul to another body to save himself. Constantine put his soul into the body of a baby, Callum Hunt. The soul belonging to Callum was forced out of its body and died in that cave. Sarah Hunt knew what happened and scrawled her message in the ice to kill the baby.
Master Joseph touches Call’s hand, and the boy sees scenes from the war and knows what Master Joseph is saying is true, even if he can’t remember it. Master Joseph has been wearing Constantine’s mask and impersonating him since the war. Master Joseph wants Call to take his place as the Enemy of Death when the time is right, so he can begin the war anew.
Call says he'll tell Master Rufus about his identity, but Master Joseph is confident that Call won’t tell and risk losing his friends and Alastair’s love. As Master Joseph is telling Call that he will let him go back to the Magisterium, the roof crashes in on them. Aaron and Tamara have come to save him. In the confusion, Master Joseph disappears.
Back at the Magisterium, Call is given the opportunity to tell Master Rufus the truth, but he lies and says the room where he met Master Joseph was empty. He decided that even if he had been Constantine once, he was still Call. He wasn’t evil, didn’t intend to hurt the Magisterium and wouldn't be told what to. He would make his own decisions.
A few days later, Master Rufus takes Call, Aaron and Tamara to pass through the First Gate, the Gate of control, signifying the end of their first year. Call knows this is his last chance to tell Master Rufus the truth and have his magic bound so he will never become the Enemy of Death. Call thinks that maybe if others find out who he is, they won’t bind his magic, but he doesn’t want to take the chance and lose the people and things he has come to love. He walks through the gate and feels the magic wash over him. He is now a mage and feels joy.