The supplementary charge sheet filed on Friday by the National Investigation Agency in the 2008 Malegaon bomb blast case, which it took over from the Maharashtra Anti Terrorist Squad in 2011, raises several questions.

On Friday, the NIA exonerated Sadhvi Pragya Thakur and five others accused of planning the operation that killed ​four persons in the Muslim-dominated Maharashtrian textile town in September 2008.Thakur was among the main accused along with Lt Col Shrikant Prasad Purohit. Purohit will continue to face trial.

This team of so-called Hindutva terrorists has been in jail since 2008, when then Maharashtra ATS chief Hemant Karkare discovered their alleged role in the Malegaon bomb blasts in September that year.

The NIA’s decision to drop the charges against Pragya Thakur was the expected conclusion of a long series of events over the last year that included witnesses turning hostile, the NIA’s Special Public Prosecutor Rohini Salian accusing the agency of pressurising her to “go soft’’ and statements of key witnesses getting misplaced.

In its new charge sheet presented before the Special Court set up to try the Malegaon blast accused, the NIA has dropped charges under the stringent Maharashtra Control of Organised Crime Act against all 14 accused, including two absconders and the nine who will continue to face trial.

Reviewing the evidence

Among the questions that arise is: were confessions by the accused to the police, and witness’ statements the only proof against Pragya Thakur? While such confessions are counted as evidence under MCOCA, they will now have no value with MCOCA charges having been dropped. In addition, even statements by witnesses made in front of a magistrate have gone missing.

But the evidence against Thakur includes a tapped telephone conversation with Ramji Kalsangra, the man who allegedly used her motorcycle to plant the bombs. After Thakur’s arrest, newspapers had reported that the Anti Terrorist Squad, which was then handling the case, had produced in court a phone conversation in which she asks Ramji Kalsangra: “Why did such few people die? Why didn’t you park [the bike] in a crowded area?”

There are also recordings of meetings held between the main accused in which Thakur features. These were recorded on the laptop of another key accused, Dayanand Pandey. Defence lawyers have claimed that these recordings have been doctored. But that’s for the court to decide.

In the face of these two pieces of evidence, it isn’t clear how the NIA made its decision to exonerate her.

Five others have been discharged along with her, for lack of evidence: Shivnarayan Kalsangra, Shyam Sahu, Praveen Takkalki, Lokesh Sharma and Dhan Singh.

The other accused

Lokesh Sharma figures as an accused in the 2007 Ajmer, Mecca Masjid and Samjhauta Express blasts, as well as the first Malegaon 2006 bomb blast. In fact, most of these cases have the same list of accused. By discharging him, the NIA is implying that Sharma had no role to play in the 2008 blasts. Is this a precursor to his exoneration in the remaining acts of terror of which he is accused?

Sharma's role in the other acts of so-called Hindutva terror has been corroborated in the confessions of Swami Aseemanand, a member of the Rashtriya Swamyamsevak Sangh. Two years after Karkare exposed the Malegaon conspiracy, his findings were vindicated when the Central Bureau of Investigation arrested Aseemanand for his role in the 2007 Mecca Masjid blasts that killed 16 persons in Hyderabad and the Ajmer blasts later that year, which killed three.

Aseemanand revealed that Purohit, Pragya Thakur, Lokesh Sharma and a small group had been responsible for carrying out bomb blasts in Muslim-dominated locations in 2006, 2007 and 2008. Amid a blaze of publicity, Aseemanand volunteered to confess in front of two different magistrates in two different cities: Delhi and Panchkula, Haryana. He has since retracted his confessions, but there was no doubt that these were made voluntarily.

Of the remaining people discharged, Dhan Singh, who is also accused in the Malegaon 2006 blasts case, had been taken by NIA officers to Malegaon to reconstruct the terrorist acts of 2006 and 2008 there. It was the NIA that had arrested Dhan Singh for the 2006 case.

Praveen Takalki, said to be a close associate of Purohit, had his bail plea rejected by the High Court in January 2014, on the ground that there was prima facie evidence against him: a confession and a corroboration of it. His confession now is useless.

So, it isn’t as if these people are peripheral players in the 2008 Malegaon blasts. Will the court accept their discharge? The problem is: who will oppose it, if the investigating agency itself wants to free them?

The exceptions

However, the cases of the remaining two people discharged on Friday fall in a different category: Shivnarayan Kalsangra and Shyam Sahu had got bail in 2011, because there was no evidence against them except for their acquaintance with the alleged bomber, Ramesh Kalsangra. These were the observations made by Justice Abhay Thipsay of the Bombay High Court while granting them bail.

Justice Thipsay’s record and reputation makes it impossible to question his decision; indeed, it is this record for steadfastness that is seen to have prompted his sudden transfer to the Allahabad High Court nine months before his retirement.

This leads to a more disturbing question. If a judge of unimpeachable integrity could have found nothing even prima facie against two of the accused, and could have granted them bail despite them being charged under MCOCA, where bail is almost impossible, it means that the ATS investigation of the 2008 Malegaon blast wasn’t flawless.

Maharashtra’s ATS has been notorious for torture from the time it was formed in 2004. Additionally, its record for nabbing the actual perpetrators of terror, is not too good.

​In the 2006 Mumbai train blasts case for which 12 Muslims were convicted last year, there were two sets of accused: the 12 indicted by the ATS, and one man indicted by the Crime Branch, who claimed his team had actually carried out the operation that left 189 commuters dead.

​The discharge last month of eight Muslim men accused in the 2006 Malegaon blasts that killed 37 has shown up the ATS also as an agency that doesn’t hesitate in fabricating cases against innocents.

In fact, human rights activists and the accused​, who had spent six years in jail for a crime they hadn’t committed, ​ demanded that ATS chief KPS Raghuvanshi should be sued for framing innocents.

A paradox

Given this record, why can’t the NIA’s charges that Hemant Karkare and his team conducted a flawed investigation in the 2008 Malegaon blasts be taken seriously? Is it because most of the accused were linked to the RSS, a holy cow even in 2008? No policeman would accuse them of terror without foolproof evidence. Karkare had gathered such evidence, much of it in the form of phone transcripts and recordings of meetings, and these had been reported at the time.

But Karkare was killed in the November 2008 terror attack on Mumbai within a month of his unearthing the Hindutva conspiracy, and Raghuvanshi took over.

There is a paradox here. Many people who hail Karkare as an honest police officer have a low opinion of Raghuvanshi because of his framing of Muslims in the Malegaon 2006 blasts. Yet, in the Malegaon 2008 blasts involving Hindus linked to the RSS, they are willing to bestow Raghuvanshi with all the credibility of a professional.

One can’t ignore what the defence lawyer in this case has been saying for some time now: the very ATS men named by the Muslims arrested in the 2006 Malegaon blasts as having tortured them have also been accused by the so-called Hindutva terror group of the same excesses.

That’s not all. The charge of MCOCA having been wrongly applied is not being made for the first time. In November 2008, when the arrests had just begun, one of the accused, Sudhakar Dwivedi alias Dayanand Pandey, whose laptop provided clinching evidence, told the MCOCA court that the ATS had extracted a confession through torture. At that stage, his lawyer declared that he would challenge the use of MCOCA, on the same grounds as the NIA has withdrawn it now. In fact, the MCOCA court itself dropped charges under this law against the accused in 2009. They were restored by the Bombay High Court in 2010, but the Supreme Court again questioned its use last year. ​

Case continues

One more point remains to be noted. Despite Pragya being exonerated, it’s obvious that the NIA isn’t letting go of all the saffron terror suspects. Yes, witnesses have been turning hostile in the Ajmer and Samjhauta blasts cases, leading one to expect mass acquittals in these too. But the most important accused – Purohit– remains charged under the Unlawful Activities (Prevention) Act, a draconian law.

Were Pragya Thakur and Lokesh Sharma exonerated because they belonged to the influential RSS? Purohit, on the other hand, is heard in the transcripts of the meetings, not only complaining that the RSS isn’t going far enough to build a Hindu nation, but is also reported by two of the accused as having plotted to kill two of the RSS’ seniormost leaders: Indresh Kumar and Mohan Bhagwat, for having received funds from Pakistan’s ISI spy agency.

Finally, are we just going to watch the NIA allow those against whom there exists a wealth of evidence of terrorist activity, to walk free? On a TV programme on Friday night, retired Justice Kolse Patil declared that he would approach the court with this evidence. He may not be alone.