Marcellus Pye was the last Alchemist and a renowned Physician who lived in the castle five hundred years in the past. He had discovered a Tincture that grants eternal life but not eternal youth, causing him still be alive while decaying and being horribly sick in Septimus Heap's time.
Septimus traveled back in time through a glass made by Marcellus and became the Alchemist's apprentice. Septimus made a new Tincture for the 500 years old Marcellus so he can be young in Septimus' time too.
When Septimus had returned to his time, he made a new Tincture for Mercellus, which reverted him to the age of 30. He then started living in Snake Slipway. His name was accidently spelled "Pie" by Terry Tarsal, who made shoes for him. Septimus badgered him for many months for Marcellus to remember what he had told Nicko Heap and Snorri Snorrelssen in his own time. Being 500 years ago, he had a hard time remembering.
In Fyre, Simon Heap became his apprentice.