A murder conspiracy that leads to a man turning into a superhero, trying to clean the system filled with corruption and injustice is what forms the premise of Mr. X. Anti-terrorist agents Raghuram (Emraan Hashmi) and Siya (Amyra Dastur) are a lovey-dovey couple who are all set to tie the knot. But a day before the wedding, the duo get busy with assignments given by their boss ACP Bharadwaj (Arunodhay Singh), wherein Raghu is sent to protect the Chief Minister from a potential threat and Siya is sent to investigate terrorists inside a hotel. Soon, Raghu realizes that it is a trap and ends up assassinating the Minister in a bid to protect his fiancee Siya, who is kidnapped at the hotel by Bharadwaj's goons. The plan masterminded by the Minister's son Aditya Dutt, ultimately leads to Raghu's capture and he is taken to a factory which is set ablaze. While he convinces the world of his death, he takes the help of his colleague Popo and his sister and lab employee Shruti Ulfat and their treatment ultimately leading to his invisibility. While he convinces Siya of his innocene, Mr. X. vows to serve justice and take revenge on the ones who wronged him.