Mumbai, Aug. 1 -- The crowd that had gathered at Malegaon's Shakeel Goods Compound on the night of September 29, 2008, for the 'isha'-the last namaz of the day, paid scant attention to the LML Freedom motorcycle bearing the registration plate MH 15 P 4572. But as the devotees bowed in prayer, two RDX bombs strapped to the seat of the motorcycle went off at 9.35 pm leaving six dead and 95 injured. This was the second terror attack in Malegaon. On September 8, 2006, on the day of Shab-e-Baraat, four bombs had gone off at the crowded Hamidia mosque complex killing 31 and injuring 312 persons. There was still no clarity on who had set off the explosions on Shab-e-baraat when the blast happened at Shakeel Goods Compound two years on. The Congress and Nationalist Congress Party alliance that governed Maharashtra in 2008 was under immense public pressure to find the perpetrators of these blasts, and handed over the investigation to the Maharashtra Anti-Terrorism Squad which was headed by Hemant Karkare. Karkare was killed shortly after in the November 2008 terror attacks in Mumbai. The first lead to the possible perpetrators came from the LML Freedom motorcycle left partially undamaged in the blast. The registration number was fake and so was the chassis number but forensic experts managed to retrieve the right chassis number and subsequently the correct registration number-- FJ-5 BR 1920. The motorcycle, they learnt, was registered in the name of a woman from Madhya Pradesh, Pragya Chandrapal Singh Thakur, who had taken sanyas and who wore a mukut (tiara) and moved around with an entourage that carried a throne for her to sit on, said a former ATS investigator. The narrative diverges here. According to the version of the ATS officer, who asked not to be named, Thakur's revelations led Karkare and his team to an obscure organisation called Abhinav Bharat with ambitions of turning India into a land of Hindus alone to be called 'Aryawart.' Its guiding force was a serving lieutenant colonel in the Indian army, Prasad Shrikant Purohit, then posted at Pachmarhi, Madhya Pradesh. Purohit's arrest led the ATS investigators to several others including a retired major Ramesh Shivaji Upadhyay, and Sudharkar Dwivedi, a self-styled Shankaracharya from Deoria in Uttar Pradesh who had recorded meetings of the Abhinav Bharat on his laptop which formed the basis of the ATS's case. Also involved was Sudhakar Chaturvedi,a resident of Mirzapur who had been seduced by Col. Purohit's call to arms. It was at his house in Deolali near Nashik that the group allegedly assembled the bombs used in Malegon. ATS claimed to have found traces of RDX and ammonium nitrate at his house. The Maharashtra ATS termed Abhinav Bharat an 'organised crime syndicate' and invoked the stringent Maharashtra Control of Organised Crime Act in the case. But the investigator who spoke to HT added: "They were a rag-tag group of people with certain ideas of a Hindu nation. They were not a big terror outfit." Coming as they did on the back of the arrest of Swami Aseemanand in the 2007 Samjauta Express blast case, Purohit and his cohort too were dubbed as part of "saffron terror", a theory that was repeatedly put to test in courtrooms and outside them. According to the version of the accused , who have now been acquitted, and their supporters, the case was built on confessions extracted through torture. In November 2008, senior BJP leader L K Advani also spoke out in Pragya Thakur's defence and sought a judicial inquiry into her allegations of torture at the hands of the Maharashtra ATS. As reported by this newspaper on November 19, 2008, Advani said that the majority community had been linked to terrorism to woo the minorities and that no community should be defamed for the sake of votes. "Just as it would not be alright to paint all Muslims as terrorists, a bad act by elements in Hindu society should not be termed Hindu terror. Fortunately, the court's decision on Thursday should put an end to that," said Nationalist Congress Party (Sharadchandra Pawar) leader Eknath Khadse, earlier with the BJP and who was the leader of a vocal opposition in the Maharashtra legislative assembly in 2008. The case got a "political colour because of the Congress-NCP government in the centre and the state and a vociferous opposition which was the BJP," added Khadse. With the formation of the National Investigation Agency after the Mumbai terror attacks of 2008, all terror cases were transferred to the NIA, including the Malegaon 2008 investigations. "Initially when NIA took over, it followed the same investigation trajectory as the ATS," says the ATS investigating officer cited above. "But investigation trajectory changed after 2014." That's a charge that has been aired publicly before too. In 2015, special public prosecutor Rohini Salian went public with the alleged pressure on her while prosecuting the case. "I was told by the NIA to "go soft" on certain key accused," she told the media then. Salian who could not be contacted was subsequently denotified by the NIA from its panel of lawyers. In its 2016 chargesheet filed in the case, the NIA dropped the provision of MCOCA, saying the conditions required for invoking the stringent law were not met. The following year the Bombay High Court granted bail to Thakur, almost nine years after she was arrested. Lt. Col. Purohit too got bail from the Supreme Court the same year. Seven other accused, including those arrested later by NIA, were discharged from the case. The two alleged bomb planters, Ramchandra Kalsangra and Sandeep Dange, were never apprehended. The remaining seven of the 16 accused in the case, including Pragya Thakur and Lt Col. Purohit were acquitted by the trial court on Thursday. Whatever be the narrative, there was just no evidence linking the motorbike to Pragya Thakur and the source of the RDX, its storage and assembling of the bomb to members of the Abhinav Bharat, the court ruled....