NIA on Wednesday filed a charge sheet against four people including Ram Chandra Kalsangra, who is absconding, for allegedly planning, conspiring and triggering blasts in Malegaon in 2006 that left 37 people dead.
The NIA filed the charge sheet in a special court in Mumbai in which the probe agency has named Kalsangra alias Ramji, a key suspect, Dhan Singh, Rajendra Chaudhary and Manohar (already in custody).
The four have been charged with murder and other sections of Indian Penal Code and Explosives Act.
The move by NIA has left Mumbai Police's elite Anti Terror Squad, which had arrested nine Muslim youths for allegedly conspiring and triggering explosion in the powerloom township located 290 kms from Mumbai, and the CBI red faced.
The NIA also sought to carry further investigations against Lokesh Sharma, Sandeep Dange and Amit Halka in this case, suspected to be activists of right-wing terror groups.
41-year-old Kalsangra, who has been declared as a proclaimed offender and also carries a cash reward of Rs 10 lakh, is alleged to be the main planner as well as the person who had strapped the cycles with explosives which were planted outside a mosque on September 8, 2006.
The agency made its breakthrough in this blast case when it arrested Chaudhary, Dhan Singh and Manmohan, who were alleged to be a part of the criminal conspiracy and touted as planter of explosives in communally-sensitive Malegaon township.
Chaudhary, according to the NIA, is one of the main conspirators and masterminds in planning and execution of the multiple blasts in Malegaon blasts.
Dhan Singh said during interrogation that he had visited Malegaon along with Kalsangra, Choudhary and Amit alias Prince on September 1, 2006 and left for Indore the same evening after a recce of target locations. Kalsangra and Amit also known as Ashwani Chauhan, are absconding, NIA said.
Manohar's role came out before the NIA during the interrogation of Chaudhary, an alleged bomber of Samjhauta train blast, who had claimed to be also a part of alleged conspiracy involved in bombing at Malegaon, the agency said.
The nine arrested Muslim youths came out of jail after nearly five years when their bail plea was not opposed.
Investigations into terror cases like Malegaon took a different turn after right-wing group Abhinav Bharat member Swami Aseemanand stated in his confessional statement before a magistrate that Malegaon blasts were executed by a Hindu group.
Aseemanand, alias Jatin Chatterjee, had stated in his statement that slain RSS worker Sunil Joshi and others were responsible for the Malegaon blasts. However, he later attempted to backtrack from his confessional statement.
Four bombs planted in Malegaon had exploded on September 8. The fateful day happened to be 'Shab-e-Baraat', considered auspicious among Muslims, when they assemble to pay respects to their departed kin.
Malegaon had seen another terror attack in 2008 allegedly by right-wing Hindu groups. Sadhvi Pragya Singh Thakur and former Lt Col Srikanth Purohit were arrested in connection with the incident.