Agathan movie tells the story of retired Major General Hareendra Natha Varma (Sathyaraj) and Gautham Menon (Dileep) who is a software engineer. His father was Mukundan Menon, a bank employee working in Srinagar. His mother was Sujatha and sister Amritha. He lost his members of the family in a terrorist attack. During that period Major Hareendranatha Varma was on duty in Srinagar.
After the incident Gautham decided to leave Srinagar. On his way to Bangalore he met a girl named Shreya (Charmi). After the journey incidentally he met Shreya several times at Bangalore. She was an MBA student. She had an inclination to Gautham. But he was least interested in loving her.
One day Shreya took him to her house. Her father Major Hareendranatha Varma, mother (Zarina Wahab) and grand mother (Valsala Menon) liked Gautham. They wished Gautham to be Shreya’s husband. One day Gautham revealed a secret to Major and story turns.