The book begins with Silas Heap finding an infant girl in the snow as he returns home with herbal medicines for his wife Sarah. Silas hides her in his cloak and takes her; on the way home, he is told by the ExtraOrdinary Wizard Marcia to raise her as his own, without telling anyone where she came from. As he returns home, the midwife runs out carrying his newborn son, Septimus Heap, pronouncing him dead. Soon after, Silas and Sarah name the baby girl Jenna and treat her as their own child.
Some years later, the ExtraOrdinary Wizard Marcia Overstrand returns and reveals Jenna to be the daughter of the assassinated queen, and takes her away for protection. However, the assassin, called the Hunter, follows them, and along with several of her family members, Marcia, and a member of the Young Army named "Boy 412", Jenna escapes to their Aunt Zelda's cottage in the Marram Marshes. In the marshes, Boy 412 discovers both a glowing ring and his own magykal powers.
Marcia attempts to return to the castle, but is captured by the guards and dungeoned for a month. While she is imprisoned, she nearly dies. Eventually, the Hunter discover where the group is staying and returns to assassinate Jenna, but he is thwarted by Aunt Zelda's freezing spell. They capture DomDaniel's apprentice, who claims to be Septimus, but he escapes and tells DomDaniel of their location.
Aunt Zelda reveals to Boy 412 that the ring belonged to the legendary Hotep-Ra, and that it gives control over the Dragon Boat: as legend goes, Hotep-Ra, the first ExtraOrdinary Wizard, was being pursued by people planning to kill him when dragon became a boat to save him. However, before Hotep-Ra died, he put the boat in a hidden temple. Later, Aunt Zelda tells Boy 412 to go in the cave where he found the ring, and Boy 412 discovers a secret cavern containing Hotep-Ra's temple and the Dragon Boat. Nicko, Jenna, and Boy 412 fly the dragon boat to save Marcia and stop DomDaniel from being the ExtraOrdinary Wizard again. They fly on the boat to DomDaniel's ship and save Marcia.
In the end, Boy 412 is revealed to be Septimus Heap. DomDaniel had ordered the midwife to take Septimus, who was the seventh son of a seventh son and expected to have great magykal powers, but accidentally ended up with one of the boys from the army nursery, leaving Septimus to grow up in the army as Boy 412.