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The story of 'The Stoneman Murders' revolves around two cops of the Bombay Police Force - suspended Sub-inspector Sanjay Shelar (Kay Kay Menon) and his professional rival Sub-inspector on duty Kedar Phadke (Arbaaz Khan). Both of them want to track down the notorious serial killer, known as the 'Stoneman'. Kedar, a laidback police officer, is officially assigned as the in-charge of the case. On the other hand, Sanjay desperately wants to catch the criminal in order to regain his repute in the Police Department and get back his job. The rivals follow their own ways to solve the mysterious puzzle.

Sanjay and Kedar are supervised by crime branch veteran AIG Satam (Vikram Gokhale). Taking into consideration Sanjay's determination and abilities, Satam permits him to investigate the 'Stoneman' case unofficially. In the process, he provides aid to Sanjay secretly, in order to accomplish the task. Kedar is unaware that Sanjay is also investigating the case. Consequently, both end up in clashes. The 'Stoneman' stalks the streets to find his prey, even as the police jostle for clues and tip-offs. The climax of the story tells who succeeds in detaining the ruthless killer.