What have courts said over the years and why has the case reached a “dead end”, leaving the families of the 31 who died in the blasts, and the 312 injured, still looking for justice?
The ATS arrested nine Muslim men, most of them Malegaon residents, after taking over the probe over a month after the blast on October 23, 2006. The agency claimed that the men were members of the banned Students Islamic Movement of India (SIMI) and also invoked the stringent Maharashtra Control of Organised Crime Act (MCOCA) against them. The ATS recorded their confessions of seven of the nine men under the Act. The men challenged the invocation of the Act, which was dismissed by the Supreme Court.
The men remained in jail from 2006, maintaining that they were innocent and were framed on the absurd allegations that they killed their fellow town residents to disrupt communal harmony. They were granted bail in 2011 after the NIA took over the probe, based on an alleged confession of Swami Aseemanand, arrested in Hyderabad in connection with the Mecca Masjid blasts.
The NIA probed the case in 2013 and said that the nine men had not committed the offence, arresting four others instead. The nine then filed for discharge.
Special court on ATS, CBI probe
The special court order came on April 25, 2016. This was over five years after the NIA took over the probe and said that a separate set of accused was responsible for the blasts. The nine men had pointed towards various irregularities in the ATS probe.
The special court said that there were some key evidences against the men that were to be evaluated while deciding on their discharge pleas. Seven of these were confessions by seven of the accused. The men retracted on the confessions later. The NIA had told court that it found in its probe that the confessional statements were recorded under pressure and force.
Another key evidence was a witness statement cited by the ATS that was recorded before a magistrate, claiming to have seen two of the accused in the godown of accused number 2, Shabbir Masiullah, along with two Pakistani nationals. When approached by the NIA as part of its probe, the witness refused to admit the statement. Two other witnesses too did not admit their earlier statements, when asked by the NIA.
The court also considered the seizure of the sampling of soil from the godown of Masiullah, taken on September 19, 2006, confirming the traces of explosive substance RDX. The court noted that the ATS case was that six bombs were assembled in the godown. Masiullah was arrested on August 3, 2006, over a month before the blasts by the ATS in another case. The court said that it was highly improbable and impossible “that the ATS which is a most competent investigating agency in Maharashtra would not have conducted raid upon the godown of accused no.2 after his arrest in a serious crime”.
The NIA also found that the independent witnesses who were claimed to have been present at the time of the collection of soil samples were not present, raising doubts over the veracity of the evidence.
The court also considered the NIA’s submission regarding the whereabouts of the accused. While Masiullah was in jail on the day of the blasts, one accused, Mohammed Ali, was in Mumbai, Dr Farogh, was in his dispensary attending to patients as seen from the register maintained by him, seized by the NIA, and one accused was in Yavatmal. An accused, who the ATS claimed wanted to become an approver, was also found to be in the ATS custody with his wife from September 13, 2006 to December 16, 2006.
“It seems to be highly impossible that the accused No. 1 to 9 who are from the Muslim community would have decided to kill their own people to create disharmony in two community that too on a holy day, that is, Shab-e-Barat,” the court then said.
While the men were discharged, the ATS filed an appeal against this special court order. It remains pending. The four men arrested by the NIA also challenged the allegations against them.
HC finds lacunae in NIA probe
In its June 2019 verdict on bail pleas by four accused, the Bombay HC observed that the NIA chargesheet was filed “by giving clean chit” to the persons booked by ATS and CBI.
In its April 22 verdict, the High Court sharply criticised the NIA probe, observing that the prosecution’s case against the four NIA-booked accused rests “solely on circumstantial evidence” and retracted confessional statements.
NIA’s case hinged largely on a statement made in 2010 to a magistrate by Swami Aseemanand, who was then an accused in other blast cases, in which he alleged that Sunil Shyamlal Joshi had told him that “his boys” carried out the 2006 Malegaon explosions. However, Aseemanand later retracted this statement, and other courts have already discarded it.
Chief Justice Shree Chandrashekhar-led bench flagged what it saw as a fundamental lacuna: the NIA neither produced any direct witnesses who saw any of the four appellants (whose appeal was allowed on April 22) engaged in bomb blasts, nor any new material that would convincingly place them there.
Instead, the bench observed that the agency “completely ignored” the earlier chargesheet filed by the Maharashtra ATS, which contained a “vivid narration” of the alleged entire planning by nine Muslim men, along with four others described as wanted accused.
The HC observed that ATS had collected incriminating material from the place of the incident and sent them for forensic examination. The Forensic Science Laboratory (FSL) reports showed the presence of RDX in soil samples taken from the blast site and from the godown of Shabbir Ahmed Masiullah (discharged by the special court in 2016), with the court noting that the samples were found to be the same and that the reports also confirmed the presence of RDX, ammonium nitrate, charcoal and fuel oil.
The bench then questioned how these scientific findings, along with voice-sample reports collected by the ATS and CBI, could be ignored by the trial court without any explanation.
It found that the special court, while framing charges against the NIA’s four accused, “overlooked the inherent contradiction and intrinsic improbability” in the NIA’s prosecution story. The two versions floated by ATS and NIA, as per HC, “cannot be reconciled by any stretch of imagination”.
Providing instances of contradictions, the HC noted that while ATS and CBI claimed the then accused Mohd. Jahid Majjid Ansari planted bombs at Malegaon, NIA said he was 400 kilometres away in Fulsawangi, Yavatmal district (Vidarbha region), on the day of blasts.
Moreover, while ATS said responsibility for purchasing bicycles (on which bombs were fixed) was with the then accused Munnawar Amin, NIA claimed Chaudhary and Narwaria bought them. The court observed the “new story of involvement of the four appellants” rested on their alleged disclosure statements.
The HC said the evidence collected by ATS is “not wiped out” from the record and “has to be considered by the trial court” even if the four appellants were required to face the trial.
The court further termed as “unreliable” the depositions of witnesses giving “two versions”. It pointed to a “mystery” about why the NIA did not collect fresh materials and instead chose to base its case largely on retracted statements of four of the nine Muslim men.
It questioned how the special judge dealt with materials collected by ATS to implicate another set of accused persons, while considering discharge pleas by four men. “The case seems to have reached a dead end,” it observed.
The blast spot at Mushawarat chowk at Malegoan. (Express photo by: Prashant Nadkar/File) 
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