The novel is set in a future world fighting over shrinking resources. Jon is born in Isoland, a vast, circular expanse of darkness, desert, storms and suffering, centred on research for the weapons and biotech industries. Separated from the rest of the world (the ?Outside?) by an insurmountable wall, test subjects are either convicts or captured from the villages of new-worlders scattered amongst the enclosed mountains. Jon is one of the taken, and his gifts will eventually transform the world but also endanger his life.
Homested, the biotech farm at the cente of Isoland, is ruled by the Vorna Dynasty. Heidi Vorna, seventeen-year-old daughter of oligarch Maxim Vorna, learns of a boy who is uniting the Isoland tribes with golden words and magical deeds. Known as the Magister, the boy appears to have other strange qualities, including an apparent resistance to the sickness used to control new-worlder populations. Preparing for leadership, Heidi is sent with Maxim?s troops to capture the boy for research. Tragedy follows as he is taken and imprisoned, leaving Heidi deeply troubled. She names him Jon Darke.
Jon grows into a resourceful and charismatic young man as three years pass. Forced to survive in the brutal conditions of Homested, his powers are growing. Heidi remains fascinated by him, but Jon blames her for his suffering and the deaths of his adoptive parents.
Maxim is both curious and fearful of Jon, and develops a strange relationship with him as teams of scientists try to discover his secrets. Amica Bright, leader of the scientists also falls for Jon, but her love is cruel and his rejection of her turns love to hatred. In return, Jon tries to teach Maxim the truth of life, but his words and actions are wasted.
In the Outside, the fight for remaining resources and viable habitats has led to war. Maxim is given orders to find a new solution and turns to Jon Darke, but Jon?s growing powers already divine what is intended, and he escapes from Isoland, heading for England. The threat of Jon falling into enemy hands is too great a risk, and death squads are sent in pursuit, led by Amica. Heidi tries to persuade her father that she can find Jon and bring him back. When he refuses, she eventually leaves and follows Jon to London.
Jon finds a world being destroyed by greed and it is not long before he has a following. When Heidi arrives at the airport, everyone is talking about the mysterious stranger and the magic of his words. She sees an advertisement for a television interview and manages to get invited, watching from the audience. He is asked if he is Christ reborn. Jon knows nothing of such things, but he does know that the interviewer?s daughter lies in a coma and tells her the child will recover. Soon after, the child awakens. Jon also warns that danger is close, but is ignored. At the end of the interview, an attempt is made on his life as a bomb explodes and kills many. Heidi escapes with Jon and persuades him to hide with her. During that time, she realises that she loves him, and begs him to stay with her. Jon cannot remain in hiding and leaves Heidi. He is able to cure children where others have failed, and his teachings are being listened to around the world. Soon, vast numbers of people are demanding change and sharing all that they have. Jon is a threat to the world order. More governments want to understand the source of his power, and Heidi cannot find a way to see him.
Jon travels to the Amazon, determined to save the last few indigenous peoples, and persuade world leaders how much they need to change. Heidi?s father makes contact with her, asking her to help save Jon. She joins with Maxim?s squad and travels with them, but learns Amica?s true intent. She plans to execute Jon as he gives a world address, broadcasting from within the burning forest. Heidi has one chance to save the man she loves, if she can persuade him to abandon his cause.
The boy is teaching and healing in one of the villages, following an attack by Maxim?s troops. Despite the suffering, many others are making their way to listen to him. The scene is being filmed from a copter, and watched by Maxim and his generals. His daughter Heidi is also watching and this chapter is seen from her viewpoint. A news report is playing, telling of a new viral war being waged on the Outside. She witnesses Jon leave the village and vanish, but has already seen inexplicable things.
Jon has returned to his own village where his adoptive parents live. He tells them he must leave them and go on a long journey. We experience his viewpoint as Jon hears voices and has glimpses of things to come, and speaks in many tongues. He tells his family that they must also leave, but they will not leave their friends. Jon has a fit and as they try to protect him, the copters arrive.
Heidi watches as Jon is taken but his adoptive parents are killed. Heidi returns to Homested with him, and sees his suffering. He tells the troops in the copter that he forgives them for what they have done, and heals the wounded. He also tells Heidi that one day, she will save the world.