Kotthu begins with a gruesome political murder, but for much of the rest of the film, politics and violence takes a back seat. It is the after-effects in the personal lives of the people involved in these acts on the ground that the script is concerned with. Women grieving for dead husbands, mothers waiting for their jailed sons and children growing up without their fathers; these are the images that keep recurring, pointing at the cyclical nature of violence and its aftermath on either side.
Goaded by the local party boss Sadanandan (Ranjith), Shanu (Asif Ali) ends up playing a part in a political murder, in retaliation for killing one of their own. However, with Shanu getting married to Hizana (Nikhila Vimal), the local leadership decides that his friend Sumesh (Roshan Mathew), who also took part in the attack, can be handed over as one of the suspects to the police, to cool down the political temperature.