It was under the leadership of Hemant Karkare, who was the chief of the Maharashtra Anti-Terrorism Squad (ATS) that the first breakthrough in the Malegaon 2008 blast case was made. The ATS claimed that the golden-coloured LML Freedom motorcycle, on which an improvised explosive device was fit, to cause a blast on September 29, 2008, in Malegaon with an intention to create a communal rift, was registered under the name of Pragya Singh Thakur, a former member of Akhil Bhartiya Vidyarthi Parishad.
Thakur was the first arrest in the case on October 23, 2008, within a month of the blast after ATS investigation led by Karkare. Followed by Thakur’s alleged interrogation, the ATS arrested 10 others including Lieutenant Colonel Prasad Purohit, a serving member of the Indian army.
Even as the investigation was in progress, Karkare, however, lost his life in the terror attack on November 26, 2008, outside Cama Hospital. The investigation continued after his death with the ATS filing its chargesheet in the case in January 2009 against 11 accused including Thakur.
Before his probe into the Malegaon 2008 blast, Karkare had also investigated blasts in theatres in Thane and Navi Mumbai in June 2008. Two men linked to a Hindutva group were found guilty under the Explosive Substances Act and sentenced to ten years imprisonment in 2011.
In 2016, while the NIA discredited the probe carried out under Karkare in the Malegaon 2008 blast case, calling it full of “lacunae” and sought to discharge Thakur, the special court refused to discharge her stating that there was prima facie evidence about her role in the blast.