Rejecting the pleas of the accused for discharge from the case, a special NIA court, however, dropped some sections of the Unlawful Activities (Prevention) Act against as well as Maharashtra Control of Organised Crime Act (MCOCA) against the accused, which is punishable by up to life in prison.
Significantly, the court dismissed NIA's contention that there was no evidence against Sadhvi Pragya, saying it was difficult to accept the claim given that her motorcycle was used in the blast.
"There is evidence to suggest that the accused number one (Thakur) had knowledge about involvement of her motorcycle," the court said in its ruling on the nine-year-old case that had raised worries of Hindu militancy gaining a foothold as a reaction to Islamic extremism.
Sadhvi Pragya "had also expressed dissatisfaction about causing less casualties in the blast. Hence it is difficult to accept submissions on behalf of the NIA and the accused number one that she had no concern with the present crime," it said.
Special judge S D Tekale, who was hearing the pleas filed by seven of the 13 accused and the NIA's application seeking framing of charges, said that charges will be framed against Thakur, Purohit, Sudhakar Dwivedi, Major (retd) Ramesh Upadhyay, Sameer Kulkarni, Sudhakar Chaturvedi and Ajay Rahirkar.
The accused will face trial now under sections 16 and 18 of the Unlawful Activities Prevention Act (conspiring for and committing/organising a terror act) and under the Indian Penal Code for criminal conspiracy, murder, attempt to murder and causing hurt besides charges under the Explosive Substances Act and Arms Act.
The charges are punishable by various prison terms up to life, and death for murder.
The NIA, while filing a charge sheet in the case last year, gave a clean chit to Sadhvi Pragya and three others -- Shyam Sahu, Praveen Takalki, Shivnarayan Kalsangra -- saying it found no evidence against them and they should be discharged from the case.
On Wednesday, the court absolved only Sahu, Kalsangra and Takalki from all the charges leaving Thakur to face trial.
Two others, Jagdish Mhatre and Rakesh Dhawde, will face trial only under the Arms Act "before concerned courts", the NIA court said.
The NIA had claimed in its charge sheet that there was no evidence of Thakur ever being part of conspiracy meetings, and though the motorcycle used in the blast once belonged to her, she had sold it much before the blast and had no knowledge of the conspiracy.
The judge, however, also noted that statements of some witnesses supported the charge that Thakur and Purohit had participated in some of the conspiracy meetings in Faridabad and Bhopal.
Six persons were killed when an improvised explosive device strapped to a motorcycle went off at Malegaon, a town with sizable Muslim population in north Maharashtra's Nashik district, on September 29, 2008, while 101 persons were injured.
The Anti-Terrorism Squad of the Maharashtra police, which probed the case initially, charged Thakur, Purohit, Sudhakar Dwivedi, Ramesh Upadhyay, Sudhakar Chaturvedi, Jagdish Mhatre, Rakesh Dhawade, Ajay Rahirkar, Samir Kulkarni, Shyam Sahu, Shivnarayan Kalsangra, Pravin Mutalik and Ramchandra Kalsangra.
According to the ATS, it was Ramchandra Kalsangra who planted the bomb, and who is still absconding. Thakur gave her motorbike to Kalsangra to plant the bomb, the ATS said.
Thakur filed a discharge plea after the Bombay High Court granted her bail in April. The NIA didn't oppose her bail application. Purohit is also on bail.
The court also said the UAPA sections 17, 20 and 23 have been dropped against all accused. These sections relate to raising funds for a terrorist organisation, being part of a terrorist organisation and aiding someone who is part of a terrorist organisation.
This part of the ruling gives relief to saffron outfit Abhinav Bharat, which was accused by Mumbai ATS of providing arms training to right-wing activists. The ATS also says Purhoit was linked to Abhinav Bharat.
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