Silas Heap stumbles upon an abandoned baby girl the same night he is told by the Matron Midwife that his newborn 7th son has died. Silas and his wife Sarah adopt the baby girl, pretending she is their own child and name her Jenna. A few months after taking in Jenna, Sarah and Silas find out that she is their missing Princess who disappeared on the same day the Queen and ExtraOrdinary Wizard Alther Mella was murdered.
10 years later, the Queen's murderers discover the whereabouts of the missing Princess. Alther Mella's ghost who has been spying on The Supreme Custodian warns his successor, the current ExtraOrdinary Wizard Marcia Overstrand. Marcia seeks out the Heaps and convinces them to flee while she takes Jenna under custody.
Returning to the Wizard Tower, Marcia and Jenna finds the young sentry Boy 412 almost frozen to death. Marcia saves him and brings him back to her rooms to heal. A few hours later Silas and his 6th son, 12 year old Nicko shows up at Marcia's place after sending the rest of his family off. Silas is determined to remain and protect Jenna. Unfortunately the Assassin appears at about the same time and the 5 are forced to flee.
The 5 sail off on a boat with a Hunter and his Pack hot on their trail. As the group continue to flee to Silas's Aunt Zelda's home in the Marram Marshes, they learn that DomDaniel, the ExtraOrdinary Wizard before Alther has taken over control of the country. Years ago, Alther had wrested the position of ExtraOrdinary Wizard from the Necromancer DomDaniel when he realized that DomDaniel had offered Alther as a sacrifice in an Incantation using Darke Magyk.
More bad news follows shortly after they arrive at Aunt Zelda's home. Sarah sends a Message Rat informing Silas that their eldest son, 18-year old Simon has gone missing as well. Concerned, Silas decides to join Sarah and look for Simon. His search for Simon leads Silas back to The Castle where he learns from Alther that Simon has been captured and is in the hands of The Supreme Custodian.
At the same time, Stanley the Message Rat returns to the Castle to find out that The Supreme Custodian has taken over the Rat Office and he is forced to bring a false message to Marcia in order to lure her into a trap. After Marcia is captured, Jenna and her companions find DomDaniel and his Apprentice at their doorstep as Simon has betrayed their whereabouts. Luckily, they manage to turn the tables on DomDaniel when they awaken the Dragon Boat of Hotep-Ra. The Dragon Boat recognized Jenna as the Queen and Boy 412 as her new Master and aids them in turning the tables on DomDaniel and rescuing Marcia as well.
With all restored, Boy 412 accepts Marcia's invitation that he become her Apprentice. In exchange for 7 years and 1 day of service, Marcia helps Boy 412 to find out his identity. To everyone's surprise, Boy 412 turns out to be the supposed dead Septimus Heap and is now reunited with his family.