A year ago, Jonah Stone learned a startling family secret. His mother is a nephilim, meaning she is half angel, half human. That makes Jonah and his younger siblings, Eliza and Jeremiah, one-fourth angel or quarterlings. As the devil, called Abaddon, sought to round up the nephilim for his evil purposes, Jonah, his siblings and other quarterlings were summoned to join God (referred to as Elohim) and His angels in battle. Jonah, Eliza and Jeremiah were sent to train at a convent with other quarterlings. In Angel School, they studied the Word of God, practiced spiritual disciplines and learned battle tactics for facing the enemy.
As Shadow Chaser begins, Jonah finds himself with the world’s biggest zit. Soon, his entire face is covered. None of the remedies he tries have any effect. Meanwhile, he seems to be getting his fellow quarterlings into trouble, causing them physical pain. Even his own mother, with whom he can speak through an angelic vortex, appears physically weak.
The quarterlings are supposed to be focusing on their mid-term exams. But Jonah continues to feel more pain throughout his body, making it difficult for him to concentrate on his studies. He and his friends take a study break and find themselves battling fallen angels in Times Square. Again, Jonah seems to be the cause of physical injury for his peers. His popularity wanes among his classmates.
Jonah hears the angelic administrators of the school mention the name M’chala. After some research, he learns this is the fallen angel responsible for disease and death. Convinced that M’chala has targeted him, he goes in search of the demon. He finds him in a hospital ICU, and a battle ensues. Jonah’s friends find him and help him escape.
The physical portion of the mid-term exams takes place in various locations around the world, including the Roman Coliseum. The quarterlings face various challenges created especially for them and their unique strengths and weaknesses. Several times, Jonah comes face to face with an encouraging man who is never named but makes him feel safe. The man does warn that Jonah will face some serious difficulty in the future. During Jonah’s last test, he comes face to face with Abaddon. Jonah tells the devil to stop terrorizing his family and friends and to take him. Abaddon talks to Elohim, though Jonah can only hear the devil’s side of the conversation. In the end, Jonah realizes Elohim has given Abaddon power to test Jonah.
Jonah comes in first in his exams, but the victory celebration is short-lived. Jonah’s mother dies at the hands of Abaddon’s demons. Jonah and his family struggle to understand why Elohim permitted this to happen, and Jonah spends months feeling angry. In the end, as he worships at church, he realizes his mother is right there with him, praising God alongside him.