The story follows (P.S. Keerthana), a nine-year-old girl living in Chennai, who is devastated to learn from her parents, Thiruchelvan (R. Madhavan) and Indra (Simran), that she was adopted. Driven by a desperate need to find her biological roots, Amudha convinces her adoptive parents to take her to war-torn Sri Lanka to meet her birth mother.

Kannathil Muthamittal explores several themes that resonate deeply with audiences. One of the primary concerns is the quest for identity. Shwetha's search for her biological mother serves as a metaphor for the universal human desire to understand one's roots and sense of belonging. The film skillfully portrays the tensions between Shwetha's adoptive and biological identities, highlighting the complexities of self-discovery.

In an interview, Ameer Sultan revealed that the idea for Kannathil Muthamittal was born out of his desire to explore the human cost of war. He was inspired by the stories of soldiers and civilians affected by the Sri Lankan Civil War and wanted to create a film that would shed light on their experiences. The director spent months researching and developing the script, working closely with his cast and crew to bring the narrative to life.