Madaari, is a story about a mysterious man with a tragic past (Irrfan as Nirmal Kumar) who kidnaps the son (Vishesh Bansal as Rohan) of Home Minister Prashant Godwami (Tushar Dalvi) from Dehradun. The minister immediately appoints CBI officer Nachiket (Jimmy Sheirgill) to investigate the case.
A 10-year-old child, Rohan, is kidnapped from his hostel. Rohan is the only son of the Home Minister. The army and the CBI storm into action. CBI officer Nachiket Verma (Jimmy Shergill) heads the case and gets restraining order from all the other security agencies to make sure that the kidnappers don't panic and kill Rohan. Initially, the case is thought of mistaken identity wherein the kidnapper might have tried to kidnap the friend of Rohan, Cheeku who was also drugged while kidnapping.
For a long time, there is silence from the kidnapper and everyone is left guessing who it might be and at the same time, the investigation is kept extremely secret, so as to keep the kidnapper(s) from killing Rohan. Behind the scenes, the security agencies try to find the location of the kidnapper without raising any kind of suspicion. Rohan is actually kidnapped by Nirmal (Irrfan Khan) after drugging him. Rohan shows his anger towards Nirmal for kidnapping him. Nirmal shows Rohan a pre-recorded video of his friend Cheeku who is in a drugged state struggling with fear. Nirmal tells Rohan that Cheeku will be killed if he refuses to co-operate with him. Nirmal keeps travelling via public transport to evade his location.
One day, the kidnapper calls the father of Cheeku to convey a message to the Home Minister that he has kidnapped his son on purpose. His demand is that he wants his son, who was lost in an act of negligence by the government, be found. It is then revealed that Nirmal had a happy family with his son, Apu (short for Apurva) after his wife left them. Apu died when a bridge collapsed on him on his way to school. Moved and depressed by his loss, Nirmal decided to seek revenge from the politicians and others responsible for the death of his son.
The news becomes a hot item in the media. Towards the end, Nirmal travels back to his house in Mumbai with Rohan, and calls a TV news channel from there and demands all those who were involved in the bridge collapse, including the Home Minister, come to his house, threatening to kill Rohan and himself if they don't. He makes the bridge contractor, the Home Minister and the ruling party's money man (Pratap Nimbalkar), confess their corrupt activities on a live broadcast on TV. Rohan indicates he understands why Nirmal did all this and Rohan and Nirmal hug before Rohan leaves with his father. Nirmal surrenders to the police and is later seen immersing the articles his son was wearing when he died in a river, while under the custody of the police. Despite a well-intentioned and intriguing story on vigilante justice and actors like Irrfan Khan and Jimmy Shergill, Madaari comes across as a stretched film.