Baby John is the remake of Tamil hit film Theri which revolves around John D’Silva (Varun Dhawan), a bakery owner who lives with his daughter Khushi (Zara Zyanna) in Alappuzha, Kerala. He is a doting father who brings her up with the right values. John forms a bond with Khushi's teacher Tara (Wamiqa Gabbi). Tara takes John's help to save a young girl from trafficking and subsequently lodged a complain with the police against a dreaded henchman, Boss (Jaffer Sadiq). Boss and his men attack John, but the latter finishes them off ruthlessly. Tara later learns that John has a past and he's none other than DCP Satya Verma, who had a wife named Dr. Meera (Keerthy Suresh). But his confrontation with Nanaji (Jackie Shroff) proves to be a turning point in his life. Hence, he decides to leave the force and live as a common man. What happens next forms the remain plot of this action-thriller film.