The 2008 Malegaon blast case has taken another turn with claims made by retired ATS officer Mehboob Mujawar regarding alleged orders to arrest RSS chief Mohan Bhagwat during the investigation. These claims have been rejected by a special court, which recently acquitted all seven accused in the case.

Mehboob Mujawar, who was part of the Maharashtra Anti-Terrorism Squad (ATS) that initially investigated the blast, has stated that he was pressured to arrest Mohan Bhagwat on directions from IPS officer Parambir Singh and other higher officials. Mujawar alleged that the objective was to create a narrative of "saffron terror". He claimed that he refused to obey these orders as he did not find any evidence linking Bhagwat to the crime. According to Mujawar, this refusal led to false cases being registered against him by the ATS.

However, Special NIA Judge A.K. Lahoti, in his over 1,000-page judgment, dismissed these contentions. The court stated that it found no merit in the claims made by the advocate for accused Sudhakar Dwivedi, who had relied on Mujawar's statements. The court also rejected the defense lawyer's argument, which was based on a statement by ACP Mohan Kulkarni, the then chief investigating officer, who said that Mujawar was never asked to arrest any member of the RSS. Kulkarni stated that Mujawar was only sent to trace two absconding accused, Ramji Kalsangra and Sandeep Dange.

The special court noted that Mujawar's statement was made before a Magistrate court and not before Special Judge AK Lahoti. The judge concluded that while Mujawar was a member of the ATS team investigating the case, the documents submitted by the defense lawyer did not provide sufficient, provable evidence to consider the claim. The court emphasized that merely presenting documents is not enough and that the claims must be proven through reliable testimony of the concerned witness.

The 2008 Malegaon blast case involved a bomb explosion near a mosque in Malegaon, Maharashtra, on September 29, 2008. The blast, which occurred during the holy month of Ramzan, killed six people and injured over 100. The case was initially investigated by the ATS, but the National Investigation Agency (NIA) took over in 2010.

On Thursday, August 1, 2025, the special NIA court acquitted all seven accused in the case, citing a lack of sufficient evidence. The accused included Sadhvi Pragya Singh Thakur, Major (Retd) Ramesh Upadhyay, Sudhakar Chaturvedi, Ajay Rahirkar, Sudhakar Dhar Dwivedi, and Sameer Kulkarni. The court dropped all charges under the Unlawful Activities (Prevention) Act (UAPA), the Arms Act, and the Indian Penal Code (IPC). The court also ordered compensation of ₹2 lakh to the families of each of the six deceased and ₹50,000 to each injured victim.

During the trial, the prosecution examined 323 witnesses, but 34 of them turned hostile, significantly weakening the prosecution's case. The court also noted that the chassis number of the motorcycle allegedly used in the blast had been wiped out and ruled that there was no reliable evidence proving that Thakur owned the vehicle.

In addition to Mujawar's claims, a witness in the case alleged that he was tortured by ATS officers to name Uttar Pradesh Chief Minister Yogi Adityanath. The special court rejected this statement as involuntary. Sadhvi Pragya also claimed that she was tortured and forced to name Prime Minister Narendra Modi, RSS chief Mohan Bhagwat, and others.

The acquittal of the accused and the rejection of Mujawar's claims have sparked political controversy, with some alleging that the investigation was carried out with the intention to defame right-wing leaders and target the Hindu community. A lawyer representing the victims' families has stated that he will challenge the acquittal in the High Court.