The story of Ajeyo takes place in a village of Assam in 1946, just some time before India’s independence and partition. Gojen Keot (Rupam Chetia), an honest yet short-tempered young man, lives alone with his grandmother. By doing some odd jobs here and there, he struggles to earn proper livelihood. He supports Gandhi and believes that once India becomes independent, social injustice will end. Though he dropped out of school, he tutors the no-caste Muslim girl Hasina (Jupitora Bhuyan). Once as a rookie participant in the freedom struggle he failed to deliver a note to a team of marching protesters against the British that caused the lives of two freedom fighters. He regularly battles ghosts of his past related to this incident.
Most of the film involves Gojen’s defiant rebellion of the richest man in town, who sees India's partition as an opportunity for land-grabbing. Gojen also fights against caste restrictions and child marriage. He helps Joba (Munmi Kalita), a Brahmin girl widowed at age 18, to elope with freedom fighter Madan Sharma (Kapil Bora) against the wishes of her father. Later he marries Hasina and leaves the village.
The story then flashes forward to contemporary Assam, as Gojen’s granddaughter (Rimpi Das), a high-ranking policewoman, is continuing her grandfather's fight against the social evils.
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