Ordinary Wizard Silas Heap walks through the forest toward his home, located within a large walled-town called Castle. Silas brings home some herbs for his newborn son, Septimus Heap, who is supposed to be a very special and Magykal child because he is the seventh son of a seventh son. On the way home, Silas discovers an abandoned infant girl in the forest. He decides to raise the child as his own, but just before Silas arrives home, he is stopped by Marcia Overstrand, the town's ExtraOrdinary Wizard. Marcia warns Silas not to tell anyone that he found the girl and to let everyone believe that the baby was born into his family. When Silas enters his home, the Matron Midwife announces that Septimus has died. The Matron Midwife quickly leaves, carrying a bundle containing Silas' deceased son. Silas places the infant girl in his grieving wife's arms, and they raise the girl as their own, naming her Jenna.
Six months after Jenna is found, Sarah Heap learns that the queen of Castle has died. Sarah's gossipy friend, Sally Mullin, says that the queen is rumored to have been shot six months ago by her own Custodian Guards. The citizens of Castle had believed that the queen was simply ill after giving birth to her baby girl. Sarah deduces that her adopted daughter must be the missing princess. Sarah and Silas determine not to tell anyone else about their baby's real identity.
Ten years later, the Custodian Guards control the citizens of Castle, and the Supreme Custodian rules them all. The Supreme Custodian is working for the evil Necromancer DomDaniel, who lives far away in the Badlands. DomDaniel does not dare come near Castle while he believes that the young princess is still alive somewhere inside its walls. An Assassin informs the Supreme Custodian that they have finally located the missing princess and that she is living with a family of Wizards. The Supreme Custodian sends his Assassin with a silver pistol to execute the entire Heap family.
The ghost of Alther Mella, an ExtraOrdinary Wizard who was killed on the same day as the queen, warns the current ExtraOrdinary Wizard Marcia Overstrand that Jenna is in danger. Marcia goes to warn the Heaps about the Assassin. Marcia explains that she is the one who rescued the baby princess ten years ago, on the night of the queen's assassination. Marcia said she knew that the Heaps would be a good family for the princess, so she left the baby in the forest where she knew Silas would find her. Eventually, Marcia convinces Silas and Sarah Heap to go into hiding with their six sons, while Marcia herself takes Jenna to Wizard Tower for protection.
At the entrance to Wizard Tower, Marcia and Jenna find an unconscious 10-year-old sentry from the Supreme Custodian's Young Army. The boy has nearly frozen to death while guarding the tower. Marcia whispers a spell to help the boy breathe again, and they bring him inside Wizard Tower with them. Silas Heap and his youngest son, Nicko, briefly visit Wizard Tower to see Jenna. The young sentry wakes up and says that his name is Boy 412. Shortly after Boy 412 wakes up, the Assassin arrives at Wizard Tower to shoot Jenna. Marcia knocks out the Assassin with a Magykal strike. Marcia, Jenna, Silas, Nicko and Boy 412 all escape from the tower by sliding down a garbage chute.
Once out of the chute, Marcia, Silas and the three children seek help from Sally Mullin. Sally directs them to go to the nearby quay, where they board a small boat and set sail to visit Silas' aunt Zelda Heap. Sally remains behind at the café she owns. A dangerous man called the Hunter arrives at the café and demands that Sally tell him where the princess has gone, but Sally refuses. The Hunter and his pack of soldiers have been sent by the Necromancer DomDaniel to capture the princess. Another man tells the Hunter that the princess has left in a boat, so the Hunter and his pack follow in a boat of their own, after locking Sally inside her café and setting the place on fire. However, it is revealed that Sally will not be harmed because Marcia gave Sally her own personal KeepSafe charm, a rare object that will preserve her from death.
Marcia, Silas and the children see the Hunter's boat pursuing them, even though it's dark. Marcia casts a fog spell. The Hunter almost detects them, before being fooled by a Magykally projected mirror image of a boat that Marcia sends off as a decoy. Marcia, Silas and the children arrive in the Marram Marshes, the place where Aunt Zelda lives, and Marcia throws the Hunter off their trail for one last time by bespelling him to jump off his own boat and into the chilly water.
The group makes camp on a marshland beach at midnight. They are joined by the ghost of Alther Mella, who tells them that the Necromancer DomDaniel has returned from the Badlands and taken up residence in Wizard Tower. Alther Mella tells a story about when DomDaniel himself was the ExtraOrdinary Wizard and she was his apprentice. Alther was chasing DomDaniel to the top of Wizard Tower one day, and they both began struggling for possession of the Ahku Amulet, the object that gives an ExtraOrdinary Wizard their power. When Alther got the amulet, DomDaniel jumped off the side of the tower to his apparent death, cryptically promising that he would return to power with the seventh of the seventh. Alther explains that the reason he was chasing DomDaniel was because he had found evidence of DomDaniel using Darke Magyk to summon a Spectre, an evil creature.
Silas transforms their boat into a couple of canoes, and the protagonists paddle on through the marsh. Silas, Marcia and the three children stay the rest of the night in a Keeper's Cottage, where Aunt Zelda lives. In the morning, the three children go outside to explore the marsh. Boy 412 separates from Jenna and Nicko and falls down a hole into a dark cave. Boy 412 finds a ring in the dark, and when he puts it on, the ring shrinks to fit his finger. When the ring begins to glow, he sees that it is shaped like a golden dragon. Boy 412 finds his way out of the cave and back to the Keeper's Cottage, where he decides to take off but keep the dragon ring and not tell anyone about it.
A message from Sarah Heap arrives at Keeper's Cottage, saying that Sarah and four of the Heap sons are safe in the forest, staying with Galen the Physik Woman. However, their oldest son, Simon, was lost in the forest, and Sarah is worried about what has happened to him. The next morning, Silas leaves the cottage, both to look for Simon and to retrieve Marcia's KeepSafe charm from Sally Mullin, because Marcia feels that she will need the charm to protect Jenna. After Silas leaves, Marcia begins to tutor the three children in Magyk. Nicko and Jenna perform well, but Boy 412 is so adept at his Magyk lessons that Marcia offers him the honor of being her apprentice. Boy 412 declines the offer because he thinks he has no real Magykal ability and that his dragon ring is responsible for the Magykal talents he has shown.
Silas fails to find his son Simon in the forest, so he returns to Castle, where he learns that Simon had snuck away to marry his girlfriend, Lucy Gringe. The Custodian Guards prevented the wedding ceremony and held Simon in the Courthouse.
Marcia, Nicko, Jenna and Boy 412 spend the next two months of winter with Aunt Zelda in the Keeper's Cottage. Marcia receives word that Silas is in Castle, so she decides to teleport herself to Castle to ask him if he has her KeepSafe charm. Marcia is caught by the Custodian Guards at the Palace Gate, and DomDaniel orders her to be thrown into a dungeon. DomDaniel steals the Ahku Amulet from Marcia, thereby increasing his power.
Simon Heap escapes from the Supreme Custodian and rejoins his father, Silas, who has been hiding in Castle for two months because the winter snow prevented him from leaving.
The Hunter finally discovers the location of the Keeper's Cottage, and he comes to attack Jenna, bringing with him DomDaniel's young apprentice Wizard. Jenna and Boy 412 escape into the marshlands and fall into the same cave where Boy 412 had discovered his dragon ring, months ago. Boy 412 puts on the dragon ring, and it glows with gold light again, allowing Boy 412 and Jenna to find their way out. They return to the Keeper's Cottage and find the Hunter incapacitated because Aunt Zelda has frozen him in place with a spell. Nicko brings DomDaniel's apprentice to the Cottage as a hostage. The apprentice manages to capture Jenna by holding a knife to her throat, but Nicko knocks him down and takes away his knife. The apprentice tells the inhabitants of Keeper's Cottage that he is a very special person because he is the seventh son of a seventh son, and that his name is Septimus Heap.
Zelda performs a Magyk ritual to see if the apprentice is telling the truth. Zelda looks into a moonlit pond to see visions of the past, and she learns that Septimus did not die, after all. The Midwife faked Septimus' death and took him to the Young Army nursery, but the spell on the pond breaks before Zelda can learn any more about what happened to Septimus. Aunt Zelda performs a memory-altering charm on the Hunter and sends him away after he no longer remembers his life as a Hunter.
During the night, the apprentice escapes from the Keeper's Cottage, and Jenna, Nicko and Boy 412 hop into a canoe to pursue him. As soon as they reach deeper waters, the children see the Vengeance, DomDaniel's famous ship. To infiltrate the Vengeance, Jenna and Boy 412 use a spell to turn themselves invisible. Below deck, they find Marcia Overstrand as a prisoner. They are unable to rescue Marcia, but Boy 412 gives her his dragon ring before they leave the Vengeance and return to the Keeper's Cottage.
DomDaniel sees the three children leaving his ship, after their invisibility charm wears off, and he pursues them. Zelda tells the three children to use a trapdoor under the cottage to escape to the cave where Boy 412 discovered his dragon ring. Once inside the cave, Jenna touches a blue and gold dragon picture that is painted on the underground cave walls. Suddenly, the cave alters and reveals a subterranean Roman temple. In the middle of the temple sits a giant boat known as the Dragon Boat of Hotep-Ra. Boy 412 has read about Hotep-Ra's history, and he tells Jenna and Nicko that Hotep-Ra was a famous wizard who towed his shipwrecked Dragon Boat to the marshes before travelling to Castle, long ago.
The three children step aboard the Dragon Boat, and the presence of Jenna, the young queen, causes the Dragon Boat to Magykally awaken. The cave begins to flood and the Dragon Boat sails out of the cave and flies toward the Vengeance. When she is close enough to DomDaniel, Jenna sends a Magykal insect called a Shield Bug to attack DomDaniel. The Shield Bug's sting hurts DomDaniel enough to knock him down, giving Marcia Overstrand an opportunity to steal the Ahku Amulet back from him. Marcia quickly boards the Dragon Boat, and she and the three children return to the Keeper's Cottage.
The next morning, the children hear that the Vengeance was stranded in the marshes and attacked by nasty marsh creatures called Brownies. DomDaniel's apprentice escapes from the wreckage of the ship and asks Jenna and Nicko for help. They bring the apprentice back to the Keeper's Cottage, but Marcia immediately recognizes that he is not the apprentice, but DomDaniel in disguise. Marcia Magykally banishes DomDaniel back to the sunken wreck of the Vengeance.
Marcia returns Boy 412's dragon ring and tells him that the ring lit up for him because he is the Dragon Master, as Hotep-Ra once was. Boy 412 now accepts that he truly is Magykal, and he agrees to be Marcia's apprentice. Aunt Zelda finds DomDaniel's real apprentice, who is almost dead, and she manages to restore him to life.
Silas, Sarah and Simon Heap come to the Keeper's Cottage to check on Nicko and Jenna and to help Marcia Overstrand conduct an official apprentice Dinner for Boy 412, in honor of his new position as Marcia's apprentice. Marcia tells Boy 412 that he may ask her for any one favor, and Boy 412 says he would like to know who he really is. Everyone goes outside to let Zelda read Boy 412's past in the moonlit water of the pond. Zelda asks the moonlight to reveal Boy 412's mother, and the pond reflects back only the image of Sarah Heap. Then Zelda asks the pond to reveal Septimus Heap, and it reflects back the image of Boy 412.
Zelda looks into the pond one more time to see all of Septimus' past, and she finds out that the Midwife who stole him was working for DomDaniel, who wanted her to find him a powerful apprentice. A Nurse in the Young Army nursery mistook the Midwife's child for Septimus, so the Midwife's son was sent to become DomDaniel's apprentice, while Septimus was left to be raised by the Young Army. The Heaps welcome their long-lost son.