| Spoiler warning!|
The following contains major plot details about the series. Turn back now and pretend like you didn't see anything! Perhaps listen to some nice music.. That's better.
The Secret is the focal point of The Secret Series, and the main cause of conflict. Everything that happens in the books is due to the pursuit of, or protection, of this secret. The Midnight Sun longs to discover what the secret is, as it is believed to be the secret to immortality. The Terces Society's main goal is to find the secret before the Midnight Sun, so that the Midnight Sun may never find out what it is.
The Secret was discovered by a court physician in Luxor, Egypt, in 1212 A.D.. When this physician was forced to tell the Pharaoh of Egypt this secret, he was executed after three days of doing so. However, a written record of the Secret survived after the physician's death; it was written on a sheet of papyrus, the physician to be buried with it. It is not known why, because no one has ever successfully deciphered the code and lived to tell the tale. Dr L. describes the Secret's bloody history in the 1st book:
"Before he died, the physician wrote his secret on a scrap of papyrus, intending the secret to be buried with him. And so it was. Until years later, when the papyrus was taken by tomb robbers. They had no idea of its value-- they may not even have read it-- but they died violent deaths soon after, and incited a forty-year war."
[...] "In the early 19th century, the papyrus surfaced in Prague, where it was purchased as a curiosity by an antiquities dealer. He gave it to an Egyptologist for translation. The Egyptologist went mad, and the papyrus was never seen again. As for the antiquities dealer, he spent the remainder of his life in a fruitless search for the Secret, until he died alone and destitute, prey to a terrible, flesh-eating virus."
Cass recovered the Secret in the 4th book but was not able to decipher the hieroglyphics in time; as soon as she held the papyrus, it disintegrated in her hands.
Cass is the Secret Keeper, and she must solely know the secret. As Cass, Max-Ernest, and Yo-Yoji continue their journey to find the secret in the final book of the series, Cass discovers what the secret is when she finally finds the mummy of the alchemist who created this secret. The mummy tells her "Why did the ibis cross the Nile? To get to the other side." Cass is shocked and does not understand. When she confronts Max-Earnest about it she is angry because she believes the secret is a joke like "How did the chicken cross the road? To get to the other side." When she confronts Pietro (the leader of the Terces society) about this he urges Cass not to tell him the secret and she must figure it out on her own for the time being because he was very upset and wished for her to leave. We discover that Dr. L (Pietro's evil twin brother) has died and Pietro says that that is ok because he will see him on l'atro lato which he explains is the other side. A side you cannot see or feel or hear or smell, but it is there. As Cass leaves Pietro she connects Pietro's revelation of l'atro lato to the secret. Cass goes back to tell Pietro but when she goes back in he is not there. His top hat is on the table which gives away that he went to the other side.
She now knows the secret is not "Why did the ibis cross the Nile? To get to the other side." but the secret is on the other side, and Cass must go there to find out what it is.
The secret is never revealed and we can assume it never will be either because Pseudonymous Bosch is not writing another book or because this series is a work of fiction.
But you can believe what you want.