In the second book we see Septimus as the apprentice to Marcia, the ExtraOrdinary Wizard. When Simon Heap, the eldest Heap brother kidnaps Jenna, Septimus goes out to search for her. He is assisted in his search by his friend Beetle. But Jenna runs away from Simon's observatory in The Badlands and makes her way towards The Port. Eventually Septimus is able to rescue Jenna with his elder brother Nicko's help from the Port but they are tracked by Sleuth, Simon's tracking ball.
They make their way to the Marram Marshes where they take the Dragon-Boat from Aunt Zelda's cottage and fly her to the Castle. But they meet Simon, flying in the sky. Simon drops a huge Thunderflash on the Dragon-Boat and it drops over Jannit Marten's Boatyard. Septimus, Jenna and Aunt Zelda are able to revive her through the Transubstantiate Triple spell.
Septimus is also in search of the long lost Flyte charm. He finds the separated charm and unites it along with the small arrow Flyte charm that Marcia had given him as a token for his apprenticeship. Eventually he is able to fly and even warns Simon never to harm Jenna again. Also, the rock that Jenna gave him at Aunt Zelda's cottage turns out to be the egg of a dragon and eventually it hatches. Septimus absolutely adores the dragon and names him Spit Fyre. The dragon for some strange reason identifies Marcia as his mummy, much to Marcia's annoyance.
Septimus rescues Marcia by identifying the shadow that has been trailing her. He also finds out that the ShadowSafe Marcia is developing contains, unbeknownst to her, the bones of destroyed Necromancer DomDaniel, which, once reassembled, try to kill Marcia. With Septimus's help, Marcia is able to Identify him and he is once again destroyed.