Makalkku movie deals with a mentally ill woman who was admitted to a mental hospital along with her baby girl. The movie starts on a rainy night when she gives birth to this baby under a Gandhi statue on the road. She is admitted to a mental hospital by the police. The woman doesn't have any sense of the fact that she was pregnant or that she gave birth to a baby girl. She doesn't remember any thing about her past and the only word she speaks throughout the film is "Killeri".
She undergoes treatment at the mental hospital under the care of Dr.Warrier (Suresh Gopi). The doctor also takes care of the baby girl whom he names Manasi (Baby Rehana). Manasi grows up in the care of the hospital staff, the inmates as well as Dr.Warrior. Her presence makes a difference to the mentally challenged inmates. Four years pass by, Manasi grows up to be cute little girl but her mother still doesn't have any emotional feelings towards her nor seems to recognize her.
At this point the law catches up as it is illegal to keep a healthy child in the mental hospital for a long period of time like four years. Now Dr.Warrior is forced to transfer Manasi to a children's institute in Cochin. His efforts to adopt her also fails. Find out what will happen to Manasi as well as Killeri.