Years have passed since Septimus Heap, formerly known as boy 412 in the army, was chosen to be Apprentice to the ExtraOrdinary Wizard, Marcia Overstrand. Since then, he and his newfound parents have moved into the palace with his adopted sister, Princess Jenna. His six Heap brothers have gone their separate ways. Nicko loves to work with boats, while Jo-Jo, Sam, Edd and Erik live in the forest. The oldest brother, Simon, has been missing since the night Septimus was chosen to be Marcia’s Apprentice instead of him.
Septimus is given the day off to spend time with his family, and he immediately finds Jenna before she must leave for her annual visit to their Aunt Zelda’s shack so she can speak with the Dragon Boat. Septimus gives Jenna a special charm that will turn anything she wants into chocolate. He also confides that he is worried about Marcia, who has a Shadow following her. He fears the dark entity is getting stronger because even he can see it now. Marcia has been seeking the help of a ShadowSafe charm to get rid of it, but the ShadowSafe charm takes months to assemble.
While Septimus and Jenna are outside walking, his long-lost brother, Simon, rides in on horseback and insists Jenna come with him. Septimus tries to convince the others that Simon is up to no good, but no one else believes him. Septimus hurries to the docks to get help from Nicko. His brother explains that a dark stranger was looking for Jenna earlier.
Septimus is convinced that Simon is bringing the princess to this unknown man. Nicko believes their brothers in the forest may be able to help them track Simon and Jenna. Unfortunately, they get lost in the woods before they can locate the other Heaps. As darkness falls, ravenous wolverines attack them. Fortunately, their long-lost grandfather, now a tree, saves them. Grandpa Benji lifts them up into his boughs and keeps them safe through the night.
Soon after Simon forced her onto his horse, Jenna realizes he is not going to bring her back to the palace. He carries her to the Badlands, and he warns her that should she try to escape, the Land Wurms, giant creatures that eat humans, will attack her. Simon leads her to his home, a cave carved out by one of the creatures. He shows her the skull of his new master, DomDaniel — the former evil ExtraOrdinary Wizard. Simon rescued DomDaniel’s bones from the Marsh and has been serving his spirit ever since.
While Simon sleeps, Jenna uses Septimus’ charm to turn the door to chocolate so she can escape. She steals Simon’s horse and tries to flee, only to be blocked by a Land Wurm. She heads up the mountain and finds Stanley, the Message Rat she once rescued. Stanley is now part of the Secret Rat Service and has been sent to bring Jenna home. She asks instead to be taken to the Port so she can find her way from there to Aunt Zelda’s, as the time for her to speak to the Dragon Boat is fast approaching.
In the morning, Septimus and Nicko find their brothers. They are also introduced to Wolf Boy, a nearly wild boy the brothers let stay in their camp. Nicko is convinced they need Wolf Boy to help find Jenna’s trail, but Septimus learns from a witch that Jenna is heading to the Port. Wolf Boy follows them anyway, and Septimus recognizes him as a friend from the army. They find Jenna in the Port, as she is fleeing from a dark stranger, who seems to be pursuing her.
They take shelter for the night, but are discovered in the morning by Sleuth, a Tracker Ball charmed by Simon. Sleuth is supposed to tag Jenna. Once Sleuth touches Jenna, Simon will know where she is at all times. Wolf Boy tries to stop the creature, but Sleuth burns him and tags Jenna, returning to Simon. The others escape and head to the Marram Marshes and Aunt Zelda’s shack.
Before they reach Aunt Zelda, Simon, who has learned how to “flye,” pursues them. He throws a Thunderflash at Septimus, trying to retake Jenna as his prisoner. Then he turns his Darke cloak into a serpent that begins squeezing Septimus to death. Wolf Boy breaks Simon’s concentration with rocks slung from his catapult, eventually hitting Simon in the eye with one of them. Simon flees and the others take refuge with Aunt Zelda. Unfortunately, Wolf Boy falls ill due to Sleuth’s Darke Magyk.
While Aunt Zelda seeks to heal Wolf Boy, Septimus is surprised when the stone Jenna gave him a year ago breaks open to reveal a dragon. Since the dragon imprinted on him, Septimus is the one who must train him. He names the dragon Spit Fire. As Midsummer’s Eve falls, Jenna goes out to talk with the Dragon Boat.
Aunt Zelda is appalled to learn that the Dragon Boat no longer feels safe with her because a Darke One is coming. She wants to return to her home in Castle. Before the Dragon Boat can return with Septimus and the others on board, Simon again attacks them. This time, Simon uses Thunderflashes to knock the Dragon Boat out of the sky. Severely wounded, she still manages to land near Castle and take refuge in a magical cave. The others leave her there and return to the palace to look for help.
Marcia sends wizards to guard the Dragon Boat, and then sends Septimus to find a book about raising dragons. When he returns to the Wizard Tower, he finds that Spit Fire has been chewing on pieces of Marcia’s ShadowSafe charm. He, Jenna and their friend Beetle soon discover that the charm pieces actually house human bones. They assemble them into a skeleton. When Marcia accidently drops the last piece, and the skull attaches to the skeleton, it begins to reanimate itself. Also, the Shadow that had plagued Marcia for a year takes on the solid form of Ellis Cackle, DomDaniel’s first Apprentice.
Marcia has only one chance to identify the skeleton properly or one touch from it will kill her. Jenna convinces her the skeleton is DomDaniel. Marcia does call out DomDaniel’s name, but Darke Magyk continues to swirl around her. Septimus realizes that Ellis Cackle is trying to help his master. Septimus transfixes the shadow and forces him away from Marcia. Once Cackle evaporates, DomDaniel’s skeleton dissolves to dust.
Simon arrives to see his Master’s defeat and learns that DomDaniel never intended to make him his Apprentice. Simon flies out the window. Septimus follows, riding on Spit Fire, with Jenna as his navigator. Simon seeks out the Dragon Boat one more time and throws his last Thunderflash at her, causing her to sink. Spit Fire hits him with his dragon spittle, and Simon falls to the ground, unconscious.
Simon is put into a secure room, while Jenna seeks out the secret Queen’s Room in the palace. She has been told she can find help for the Dragon Boat there. Unknown to her, she is watched by her mother’s ghost. Jenna finds a passage to Aunt Zelda, who has the power to heal the Dragon Boat.
While Septimus waits for Jenna to leave the Queen’s Room, he realizes that the Flyte charm he took from Simon connects with the silver winged charm Marcia gave him some time ago. Together, they form the completed Flyte charm, which gives the owner greater control while flying.
Jenna returns with Aunt Zelda, and the three make their way to the Dragon Boat. They use a special charm, in which Aunt Zelda calls on the powers of the earth, Jenna on water and Septimus on air. Their Magyk heals the Dragon Boat.
When they all return to the palace, Jenna is horrified to see the Dark Stranger, who had followed her earlier. Marcia gives the man a hug. She explains that the man’s name is Milo, and he is Jenna’s father. He was told that both his wife and Jenna had been murdered so he took off for a life on the sea to escape his grief. When he learned that Jenna was alive, he made his way back to the palace.
As life returns to normal, Simon escapes from his cell. Septimus uses his new Flye ability to find him. He lets Simon go with the warning never to try and hurt Jenna again.