Vilaapangalkkappauram movie begins with the young and beautiful Sahira (Priyanka) who is living in Gujarat along with her parents. While his father Yusuf is a Muslim from Kerala, her mother is Nargis who is based in Gujarat. Sahira also has a darling sister Shamla and it is one small happy family.
However Yusuf always has the longing to get back to his homeland Kerala and keeps sharing with his darling daughter Sahira. But as fate would have it, riots break out in Gujarat and Sahira's family is destroyed, she is brutally raped and is left to die but then despite her condition she manages to bring strength and escapes from there.
To her luck she gets on to a truck that goes to Kerala and by the time she reaches there she is in a mess. Sahira gets admitted into a hospital and is taken care of by Doctors Mary (Suhasini) and Gopinath (Biju Menon).
However, the story of Sahira starts making rounds and in no time a set of politicians, rights activists and others start troubling her just to get a piece of their own meat and publicity. Despite the pressures, the doctors finally manage to treat Sahira and make her recover but then her mental trauma is still not cleared.What happens from there forms the rest of the story