In "Physik" we find that when Silas Heap and Gringe the gatekeeper accidentally sets free the spirit of an evil Queen Etheldredda, everything seems to be in trouble. The Queen sends Septimus to her 500 year old son Marcellus Pye who drank the potion of Immortality. The old Marcellus then sends him back in time to the young Marcellus Pye and there Septimus becomes his apprentice and learns about "Physik". Marcia learns about Septimus' departure from Marcellus's book I, Marcellus in the Wizard Tower library, when she finds a page, 500 years old with Septimus's writing in it.
Jenna and Nicko, with Alther Mella and Alice Nettles help try to find Septimus. They meet Snorri Snorrelssen, a Northern Trader girl. Together they fall off through a glass into the past 500 years back. There Jenna is mistaken for the lost princess Esmeralda and dragged to her mother, the living Queen Etheldredda. She somehow manages to run and finds Septimus. Together all of them try to pass back through the doors of time, but Etheldredda and Marcellus come in arguing about when the Queen have the Drink of Immortality. Although Marcellus warns the Queen that the drink is incomplete, she nevertheless drinks it.
They then discover Jenna and the others hiding in the Alchemie Chamber and Etheldredda drags Jenna to drown her but in the process she herself gets drowned. Since she drank the incomplete potion her spirit has an incomplete form neither rending it immortality nor, a complete Spirit. Septimus, Jenna, Nicko and Snorri's cat Ullr then start their journey through the Doors of Time but Nicko runs away in search of Snorri.
Septimus and Jenna return to the Castle, much to the surprise and delight of Marcia Overstrand, who welcomes her apprentice back with an enormous hug. But Etheldredda's ghost tries to kill Jenna with the I.P (Infant Princess) bullet that was named for Jenna by the Assassin in Magyk. She is about to shoot the bullet when Alice Nettles hurls herself in front of Jenna and the bullet kills her. Marcia then draws a BoneFyre from Spit Fyre's fire and destroys Etheldredda's portrait hence Etheldredda and her pet, the Aie-Aie, which had caused a Sicknesse all through the Castle, are finished. Septimus, with his Physik knowledge is able to brew up an antidote for the Sicknesse and soon all is well. He promises to make a potion for Restoring youth for Marcellus and in return Marcellus would give him back his Flyte charm.