SHAB-E-BARAT is considered among the holiest nights by Muslims. Like thousands around the world, the Muslim community in Malegaon, a town 300 kilometres from Mumbai, observes this night with fervour and reverence. In 2006, as the community prepared to attend the prayers, a series of powerful bombs exploded at Mushawerat Chowk and Bada Kabrastan in the congested Muslim quarter. Thirty-seven people died and over 300 were injured. It is widely believed that had the blasts taken place later in the evening, when the prayers were to begin, the death toll would have been much higher. Within days of the blasts, nine Muslim men from the town were arrested.

A decade later, on April 26, a sessions court in Mumbai acquitted all of them. The judge, V.V. Patil, said: “In my view, the basic foundation or the objective shown by ATS [Anti-Terror-Squad] behind the blast is not acceptable to a man of ordinary prudence. I say so because there was ‘Ganesh immersion’ just prior to September 8, 2006…. Had accused No. 1 to 9 any objective that there should be riots at Malegaon, then they ought to have planted bombs at the time of Ganesh immersion which would have caused death of most Hindu people. It seems to me highly impossible that accused No. 1 to 9, who are from Muslim community, would have decided to kill their own people to create disharmony between the two communities, that too on a holy day i.e., Shab-e Barat.”

The judge noted that there was not sufficient ground to proceed against the eight men (the ninth accused, Shabbir Masiullah, died in an accident early last year) and ordered that they be “set at liberty”.

The complete story behind the blasts may take time in emerging, but this case once again reflects how flawed India’s investigation process is when it comes to cracking terror cases.

It also brings to the fore divisive political agendas and highlights severe human rights violations.

Nine men languished in jail for five years (they were granted bail in 2011) with no defence. Most of them were too poor to afford legal help. In fact, one of them could not come to Mumbai for the acquittal hearing because he could not afford the fare.

Their innocence was proved only because investigative agencies did not have enough evidence. It needs to be asked why it took 10 years to reach this conclusion.

In this time, lives have been scarred and entire families destroyed by crimes in which they were not involved.

Is there any provision to compensate for the time lost? Further, why were they not set free when evidence emerged to implicate others for the crime?

The Malegaon blasts case is a murky one with multiple layers of complexity. It led to the discovery of a sinister plot involving Hindu fringe groups, which eventually led to the exposing of rising saffron terror in the country.

In spite of evidence leading to Hindu extremist groups in the terror plot, the Malegaon accused remained in jail for many years. The ATS did not drop the accusations against them. It was only after the National Investigation Agency (NIA) took over the probe in 2011 and said there was little evidence to prosecute them that they got bail.

According to a source in Malegaon, the ATS, in complicity with the local police, who were clearly under pressure to produce answers after the blasts, decided to pick up nine local residents on cooked-up charges. “Some of these men were targets of local rivalries, others had vague links to people connected to organisations. One of them just had a name that sounded similar to that of another wanted man,” the source said. The “conspirators” were too poor and scared to fight their cases. The police allegedly told them that any relatives they tried to contact would be killed. They were also told that people in Malegaon were angry and would kill them if they came back. “These men are not empowered or equipped to take on the establishment. Confessions were apparently forced and torture was part of the process,” the source said.

Finally, the Jamiat Ulema-e-Hind in Malegaon put together finances and arranged legal assistance for the accused.

Maulana Abdul Hameed Azhari, who had helped the men in their legal battle, said: “The fact is that these men were framed. The police had no answers and therefore caught some Muslims and charged them. When the truth about saffron terror came out, they were still not released. That is injustice and a violation of human rights. If you look at their profiles, not one would seem to have a terror background.”

Mubasshir Mushtaq, a local journalist who has followed the case, said the ATS shamelessly tried to build a fictitious case against the men but failed miserably. “Some of these men got into trouble because of false information given by people who had petty grievances.”

A year before the Malegaon blasts, explosives were found at the homes of members of Hindu extremist groups in different parts of Maharashtra. In Nanded, two Bajrang Dal workers had died while assembling explosives. Some mysterious blasts had taken place in Parbhani, Purna and Jalna and there were murmurs of Hindu right-wing activists attempting terror strikes. In December 2006, the ATS filed a charge sheet against the nine men they arrested under MCOCA (Maharashtra Control of Organised Crime Act, 1999). There was reportedly much anger against the police in Malegaon, particularly against Superintendent of Police Rajvardhan Singh, who reportedly framed people. The Central Bureau of Investigation (CBI) then stepped in but filed only a supplementary charge sheet and then, curiously, moved away from the investigation.

In 2007, when Shabbir Masiullah (he died in an accident last year) filed a writ petition in the Bombay High Court questioning the constitutional validity of MCOCA, the Malegaon case went into a spin. After the High Court dismissed his petition, Masiullah appealed in the Supreme Court. Unfortunately, his lawyer, Shaheed Azmi, was shot, reportedly by a hitman from the Mumbai mafia. The Supreme Court, after hearing the case, reserved judgment for a year. Eventually, in 2011, the apex court asked the NIA to investigate the case.

From 2007 to 2008 several things happened that changed the tone of the case. Attacks took place on the Samjhauta Express (February 2007), the Mecca Masjid in Hyderabad (May 2007), the Ajmer Dargah (October 2007) and once again in Malegaon in October 2008. A pattern was emerging.

A decisive breakthrough came in September 2008 when Hemant Karkare, the ATS chief who was gunned down in the 26/11 Mumbai terror strike, chased a lead on the ownership of a motorbike that held the explosives. The bike was traced to Sadhvi Pragya Singh Thakur, and investigations now held pointers to a Hindutva plot.

Evidence led the police to Sadhvi Pragya Singh Thakur, Sameer Kulkarni, an Abhinav Bharat member, and to Lt Col. Shrikant Prasad Purohit, a serving army officer. Purohit apparently provided the RDX (Research Department Explosive) for the bomb and masterminded the operation along with one Ramji. The news sent shockwaves across the country.

In 2009, the ATS, under K.P. Raghuvanshi, filed a 4,528-page charge sheet that included extensive details on the real conspirators and on the planning and execution of the Malegaon blasts. Still, the case against the nine “conspirators” who were arrested in 2008 remained in limbo. Swami Aseemanand, who was arrested for the Samjhauta Express blast, made a stunning confession in 2010. He told interrogators that he and other Hindu activists were involved in bombings at various Muslim religious places as they wanted to answer every Islamist terrorist act in kind with “a bomb for bomb’’ policy. He later retracted his statement. But the magazine that broke the story corroborated the information with audio tapes.

Interestingly, when the NIA took over the case, it absolved the nine accused saying there was insufficient evidence to link them to the bombings. It booked four Hindu extremists, Lokesh Sharma, Dhan Singh, Rajendra Choudhary and Manohar Narwaria, in the case. A week before the MCOCA court was to hear the discharge pleas of the Malegaon nine, the NIA reversed its stand and said the discharge could not be allowed.

“We aren’t sure why this happened given how clear the NIA was in concluding that the accused were not involved in the bomb blasts,” said a rights lawyer. “We suspect political pressure, but that has been a problem with this case ever since the Hindu fundamentalist angle was exposed,” he said.

Recently, the public prosecutor in the case, Rohini Salian, said she was asked by the new government to “go soft” on the accused of the 2006 Malegaon case. Last year, she filed an affidavit initiating contempt proceedings against the NIA for “tending to hamper the judicial process”, resulting in “weakening of the prosecution’s case”.

The Malegaon blasts case runs deep. The false charges against the nine men form just the tip of the iceberg.