Nine persons were killed in a powerful explosion that ripped through the mosque on May 18, 2007.
The chargesheet also mentioned that Aseemanand made a confessional statement before a metropolitan magistrate in Delhi.
The Mecca Masjid blasts have often been called the first instance of the much debated "Hindu terror" in India.
Two other accused, Sandeep V Dange, former RSS pracharak and Ramchandra Kalsangra, electrician-cum-RSS activist, also from Madhya Pradesh are still eluding the investigators. This claim was supported by Rohini Salian, public prosecutor for the state of Maharashtra, who, in June 2015, had told The Indian Express that officials of the NIA had told her to "go easy" on the 2008 Malegaon accused. The investigation against Parmar and Chouhan is continuing. After a thorough investigation, the case has been transferred to the CBI. It remains to be whether BJP comes with a remark on the acquittal of Swami Aseemanand or not. Nearly all of them were detained at a guest house where they alleged torture at the hands of SIT.
10 people were named as accused in the case.
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The NIA took over the case on 7 April 2011.
The Mecca Masjid case has faced several setbacks. The prosecution relied on bomb comparison of both Ajmer and Mecca Masjid blasts. Right from beginning we had been placing before the court that this is not the statement of confession.
"Indreshji met me at Shabri Dham (Aseemanand's ashram in the Dangs district of Gujarat) sometime in 2005".
Charges were filed against Aseemanand, Sunil Joshi, Devendra Gupta, Lokesh Sharma, Chandrashekhar Leve, Harshad Solanki, Mehul Kumar, Mukesh Vasani and Bharat Bhai. Five others were shot dead by police during a riot that followed.
Swamy Aseemanand, a resident of Gujarat and head of Vanvasi Kalyan Ashram, was earlier acquitted in the Ajmer Dargah blast case and is now on bail in Samjhauta Express blast case of 2014.
Owaisi had on Monday slammed the NIA for "not pursuing the case" and alleged that the elite investigation agency was not allowed to do so by the "political masters". Out of these, 54 witnesses now turned back from the testimony.