Following their recent acquittal in the 2008 Malegaon blast case, several individuals have come forward with allegations of torture and coercion during the investigation, claiming they were pressured to falsely implicate prominent political and religious figures. These figures include Uttar Pradesh Chief Minister Yogi Adityanath, Rashtriya Swayamsevak Sangh (RSS) chief Mohan Bhagwat, and even Prime Minister Narendra Modi.

Major Ramesh Upadhyay (retd), one of those acquitted, stated that he faced severe physical and mental torture while in custody. According to Upadhyay, officials repeatedly pressured him to name Adityanath, Bhagwat, and RSS leader Indresh Kumar in exchange for leniency and early release. He alleges that the investigation was politically motivated and influenced by the then-UPA government, with officers acting under pressure from leaders like Sonia Gandhi, Digvijaya Singh, and Sushilkumar Shinde. Upadhyay claims he never visited Malegaon and had no connection to the incident. Despite the hardships he faced, he refused to give a false statement and fought to prove his innocence.

Similarly, Pragya Singh Thakur, a former BJP MP also acquitted in the case, has made similar accusations. Thakur alleges that the Anti-Terrorism Squad (ATS) tortured her and forced her to implicate Narendra Modi, Yogi Adityanath, and Mohan Bhagwat. She claims that the Congress party orchestrated a conspiracy against her. Thakur, who spent nearly nine years in prison, said she was detained illegally and subjected to intense pressure to implicate senior BJP and RSS leaders. She stated that officials told her the torture would stop if she complied with their demands.

These allegations follow the NIA court's acquittal of all seven accused in the 2008 Malegaon blasts, citing a lack of evidence. The court also ordered the Maharashtra government to provide compensation to the victims' families. The 2008 Malegaon blast case pertained to an explosion that occurred in Malegaon, Maharashtra, near a mosque during evening prayers. The initial investigation blamed Islamic militant groups, but later shifted to alleged Hindu extremist groups, leading to the arrests of Thakur, Upadhyay, and others.

These claims of torture and coercion have sparked controversy, with those accused maintaining their innocence and alleging political motivation behind the investigation. The allegations raise questions about the integrity of the investigation process and the potential for political interference in law enforcement.