Silas Heap does not realize the trouble that will follow when he accidentally lets out the ghosts of Queen Etheldredda and her pet Aie-Aie from a Sealed Room. Soon the residents of the Castle start falling ill from a strange Sicknesse
which no one knows how to cure. Then, Etheldredda's ghost tricks her descendant Princess Jenna into inadvertently sending her adoptive brother, Septimus Heap into the past.
Septimus finds himself 500 years in the past as the unwilling Apprentice to the Last Alchemist,
Marcellus Pye who also happens to be the son of the then Queen Etheldredda the Awful. Marcellus needs the help of a 7th son of a 7th son in order to complete his tincture for both Everlasting Life and Everlasting Youth in order to prevent the terrible fate which awaits him. He is doomed to spend the next 500 years rotting as he drunk an incomplete tincture, and has Everlasting Life but not Everlasting Youth.
Meanwhile, a distraught Jenna who fears the worst after seeing Septimus disappear into the mirror in the Queen's Robing Room attempts to find Septimus using Spit Fyre after she is advised that dragons are able to find their Imprintors wherever they are. Spit Fyre's Seek
brings Jenna and her brother Nicko to Warehouse Number Nine, home to Chief Customs Officer Alice Nettles, where they find another of Marcellus's Glass of Time. Jenna, Nicko and their new friends, the Spirit-Seer and Northern Trader 14-year old Snorri Snorrelsen and her pet Ullr a Night Creature and Spirit-Seer Cat, travel through the Glass and arrives 5 and a half-months after Septimus's arrival in Marcellus's time.
While searching for Septimus, Jenna is mistaken as the supposedly dead Princess Esmeralda
and learns that Esmeralda faked her own death with the help of her brother Marcellus and then Keeper of the Dragon Boat, Broda Pye. Esmeralda did this to escape from her mother, Queen Etheldredda who intends to kill Esmeralda as she did Esmeralda's baby twin sisters.
Once Jenna, Nicko, Snorri and Septimus are reunited they attempt to escape through the Great Doors of Time
in the Great Chamber of Alchemie and Physik. Unfortunately they are discovered and Jenna is almost killed by Queen Etheldredda. Jenna escapes but Etheldredda herself drowns.
Septimus strikes a bargain with Marcellus with Septimus agreeing to create the tincture to give Marcellus Everlasting Youth once Septimus returns to his time. Septimus, Jenna and Ullr return
to their own time but Nicko and Snorri is left stranded in the past when the Great Doors of Time become unstable.
In their own time, Septimus brews the tincture needed to cure
those ill from the Sicknesse and Marcia gets rid of the troublesome ghosts of Queen Etheldredda and her Aie-Aie.