Doctor Innocent aanu is the story of Homeopathic Doctor Bargavan Pillai (Innocent), who always helps poor patients. His wife Subha lakshmi (Sona Nair) is unhappy that her husband is not earning a lot to lead a financially healthy life. For the Panchayat elections, one political party approaches Bargavan Pillai to contest on behalf of them. Though he was reluctant, his relents finally as his wife persuades him into it. But Doctor does not win the elections even after a strong campaign.
Bargavan Pillai's long friend Dr. James (Devan) invites them for his daughter's wedding. Subha Lakshmi complaints that the family do not have good dresses to wear for the wedding. Bargavan Pillai goes to a pawn broker and takes money instead of his beloved scooter. His family becomes excited when they get new dress but now Subha Lakshmi complaints that they do not have enough ornaments. On her advice, Doctor goes to his neighbor Vasudevan (Suraj Venjaramood) and borrows his wife's costly necklace for a day. But Subha Lakshmi loses the ornament during the marriage. Doctor buys a new ornament from a Jewellery shop by promising that he will pay the money in a few days and gives it to Vasudevan.
Dr James comes to Bargavan pillai's home to say that he got the ornament back from the garden. Bargavan pillai goes to the Jewellery shop to give the ornament back and clear the debt. But they find that the ornament is only gold plated. Bargavan pillai comes to Vasudevan's house only to see that Vasudevan has been arrested by police for similar frauds. Bargavan pillai also comes to know that the politicians who stood with him during the elections had taken loan from a bank using Bargavan pillai's signature.
Since Bargavan pillai hadn't repaid the loan for a long time, Bank decides to seize his house. But during the court proceedings of sealing his house, Anna (Nithya Menon) comes to the scene. She was brought up at the orphanage where Bargavan pillai was giving free service all these years. Anna says she is alive only because of the medicines Bargavan pillai send her. Anna promises to clear off his debts and all ends well.