Roja revolves around one Man's love for his motherland and a wife's unfailing love for her husband. Roja (Madhoo) is a village girl, born and brought up in Sundarapandianpuram in Tirunelveli district in Southern Tamil Nadu. She prays that the handsome suitor and top cryptologist Rishi Kumar (Arvind Swamy), arriving in the village soon, accepts a proposal to get married to her sister.
It soon emerges that Roja's sister is in love with another, and to everyone's surprise Rishi requests Roja's hand in marriage. Being unaware of her sister's love affair, Roja is not willing to accept Rishi's proposal as she believes that he is the best match for her sister. But due to her parent's pressure, she gets married to Rishi, and the couple move out of the village to live in Madras. Initially Roja is angry with Rishi for rejecting her sister but when she comes to know that it was her sister's own wish to marry her love rejecting Rishi, she apologizes and starts to fall in love with Rishi.
Working for the Indian Government, Rishi is assigned a posting at an army communications center in Kashmir. In here Roja's world gets shattered when Rishi is abducted by the terrorists from Pakistan who are fighting for Kashmir and demanding the release of their terrorist leader Wasim Khan from prison, held by Indian military forces. Roja pleads with politicians and the military for help, Where as Roja doesn't know the other languages much.
She tries to convey the military officials and politicians in different ways that what pain she receives after her hubby's abduction. but it all goes in vain. What happens to Rishi and Wasim Khan forms the rest of the story.