The film starts off with an introduction of Joint Director Ashwin Kumar at the annual function of India's premier police investigating agency, the Central Department of Investigation (CDI). At the function (1 April 2008), his senior officers hand him over a double murder case. The film then goes into a flashback of events leading to the murders.
On the night of 15–16 March 2008, Shruti Tandon (Ayesha Parveen), a 14-year girl is found dead at her home in Sameer Vihar of Noida, by her parents Ramesh (Neeraj Kabi) and Nutan (Konkona Sen Sharma). The local policemen, led by Inspector Dhaniram (Gajraj Rao) are incompetent and do not know the basics of a criminal investigation. Initially, they seek the missing servant Khempal. However, later, Khempal's decomposed body is found on the terrace of the building in which the Tandons live. The police question Khempal's close friend and Tandons' assistant Kanhaiya. Kanhaiya tells the police that Ramesh Tandon might have been involved in an extra-marital affair, and Khempal might have been involved in a relationship with Shruti. The police start suspecting the Tandons, and after sometime, declare the murders as a clear case of honour killing. On 25 March, the Noida police arrest Ramesh Tandon for the two murders. The police chief organizes a press conference in which he declares that Ramesh murdered Shruti and Khempal after finding them in a compromising position. This character assassination of Shruti leads to public outrage, and the case is handed over to the Central Department of Investigation (CDI), the country's elite investigating police agency.
The CDI team is led by Joint Director Ashwin Kumar (Irrfan Khan) and ACP Vedant (Soham Shah). Kumar holds contempt for the sloppy first responders who botched the initial crime-scene investigation. He believes the parents to be innocent, and methodically builds a case against the father's resentful assistant. His team uses narco tests, attempting to prove that the assistant and his two accomplices committed the murders. On 22 June 2008, he officially exonerates the parents, and Ramesh Tandon is released from the jail.The narrative also briefly discusses the dissolution of Kumar's marriage with Reema (Tabu).
Just as Ashwin Kumar is about to conclude his investigation, his senior officer retires and a new CDI chief takes over. ACP Vedant, in his greed to get a promotion, starts working against Kumar. This leads to an altercation between the two officers, resulting in Kumar's suspension. On 9 July 2008, CDI hands over the case to a new probe team led by Kumar's former boss Paul (Atul Kumar), who concludes that the parents committed the murders. In the final act, rival camps (of Kumar and Paul), with opposing hypotheses, make their cases before the CDI chief. On 20 February 2011, CDI files a closure report in Ghaziabad court, naming parents as the prime suspects, but states that the evidence is insufficient to initiate prosecution. On 15 March, the Tandon's file a protest plea opposing CDI's report. On 25 March, the judge rejects the closure report and makes the parents an accused in the case. The trial begins on 8 June 2012, and the Tandon are convicted for the murders on 26 November 2013.