After losing their ancestral home to Arackal Madhavanunni, Shivaraman Nair seeks the help of his trusted lieutenant, Nedungadi, in order to kill Arackal and get their house back.

Secret promises to be a gripping tale that explores the science of omens (Nimitha Shasthram), psychological turmoil, and the strength of friendships.

The story revolves around the clash between Ayyappan, a senior police officer who serves at the Attappadi Police Station and Havildar Koshi, who comes to the village with a motive.

The story is set against the backdrop of hills of Nilgiris where two siblings, Joshua and Jenny, who come from a middle-class family. Together, they dwell on the serenity and calmness of the mountains.