Malsaram movie is based on the story of Kupikundam Hamsa (Kalabhavan Mani) who is the illegitimate son of Achum Kundam Thomacha (Vijayraghavan). Hamsa's mother is a mentally deranged lady. Hamsa bears a grudge against Achum Kundam Thomacha and keeps on troubling him all the time.
Achum Kundam Thomacha's daughters are on the side of Mani. Achum Kundam Thomacha gets his son in law a Circle Inspector to come on transfer and get Mani controlled but this too fails. The son in law then gets a killer from Chennai to bump off Mani. The killer is a look alike of Mani. A struggle takes place and the killer is stabbed to death.
The public thinks that Hamsa is dead. Mani now with Hanifa takes the place of the killer. Achum Kundam Thomacha gets angry with his son in law for selling off properties without his knowledge and disowns him. The son in law once again goes to Chennai and tells Mani to kill Achum Kundam Thomacha without realising his true identity. Now father and son unite against a common enemy.