Kutty Srank, which translates to "junior boat captain" in Malayalam, presents the life of a mariner operating a cargo ship near Kodungalloor, a once-thriving port town in Kerala. The film starts with the local police discovering an unidentified body that has washed ashore. Amidst the intrigue, a Buddhist nun, Revamma, steps forward, claiming she can identify the corpse, asserting that it belongs to a man known as Kutty Srank. This prompts the police to investigate her connection to him.
As the story unfolds, a Latin Christian woman, Pemenna, also claims to recognize the deceased. Both women are adamant in their conviction that the body is indeed that of Kutty Srank. Their claims spark debate when a mute woman named Kali, who is later revealed to be Kutty Srank's wife, arrives to view the body. She disputes the other women’s assertions, insisting the corpse does not belong to him.
The narrative takes us into flashbacks where Revamma recounts her past and her ties with Kutty Srank. Her father, Moopan, is portrayed as a notorious local don with a blood-drenched history. In her recollections, blood serves as a prominent motif. Following her return from studying abroad, Revamma defies her father's expectations by announcing her conversion to Buddhism, which incites his wrath. Moopan then engages Kutty Srank in a sinister scheme involving the disposal of a Buddhist monk who had been with her. However, Kutty Srank's steadfast loyalty to Moopan falters when he faces this betrayal, leading Revamma to manipulate his confusion in a bid for her freedom.
The film beautifully explores the complex relationship between Mammootty as Kutty Srank, and Revamma's deteriorating mental state, marked by irrational behavior stemming from her traumatic past. The only characters showing a semblance of normalcy are Revamma's aunt and uncle, who are portrayed as concerned for her well-being, attempting to manage the chaos brought about by Moopan.
Their escape eventually leads them near Cochin, where Kutty Srank has an unexpected reunion with Pemenna. She reveals that he used to work as a ferryboat captain in her village, having left under questionable circumstances. Their connection is further explored as he becomes friends with Loni, played by Suresh Krishna, who invites him to participate in a local performance of Chavittu Nadakam focused on the Holy Roman Emperor Charles the Great. This event allows Kutty Srank to display a more jovial side, revealing moments of laughter and camaraderie despite the underlying tension from his past.
However, the spirit of camaraderie is disrupted by the local priest, who sees Kutty Srank as a threat, stirring jealousy and distrust among the villagers. As the narrative intensifies, conflicts arise, with Moopan's henchmen reappearing, and the atmosphere thickening with impending violence. Kutty Srank finds himself once again at a crossroads, navigating betrayal and the fallout of past decisions.
The conclusion brings in Kali, who has been living with an elderly woman capable of interpreting her signs, identified as Kutty Srank's pregnant wife. She shockingly asserts that the body does not belong to him. The final flashbacks reveal her narrative, commencing from the time Kutty Srank has tried to evade Moopan’s clutches again. He becomes entangled with Unnithan, a character disillusioned by tragedy looming over his family. Faced with yet another moral dilemma, Kutty Srank chooses compassion over ruthlessness when confronted by Kali's plight.
Ultimately, the story showcases their treacherous journey, culminating in a tense spectacle back in the village with the play that must go on, solidifying Kutty Srank's legacy and intertwining the lives of these women forever.
