In a sharp rebuke to the National Investigation Agency (NIA), the Bombay High Court has said the 2006 Malegaon blasts case has "seems to have reached a dead end," while discharging four accused and questioning how crucial evidence gathered by earlier investigators was overlooked.

The high court’s order on Wednesday also left unresolved the question of who was responsible for the serial explosions that killed 31 people.

The four discharged accused are Rajendra Chaudhary, Dhan Singh, Manohar Ram Singh Narwaria and Lokesh Sharma. The court said there was insufficient evidence to make them stand trial in the case.

They had been charged under Indian Penal Code provisions related to murder and criminal conspiracy, along with the Unlawful (Activities) Prevention Act (UAPA).

The HC also quashed a September 2025 special court order framing charges against them, stating the judge had not "applied his mind".

On September 8, 2006, four bombs exploded in Malegaon town of Maharashtra’s Nashik district. Three blasts took place inside Hamidia Masjid and Bada Kabrastan shortly after Friday prayers, while the fourth occurred at Mushawarat Chowk. The explosions killed 31 people and injured 312 others.

A bench of Chief Justice Shree Chandrashekhar and Justice Shyam Chandak said the NIA had "completely ignored" the probe and chargesheet filed by the Anti-Terrorism Squad (ATS), which had detailed an alleged conspiracy involving nine Muslim men arrested earlier in the case.

The investigation saw dramatic shifts over the years. Initial agencies alleged the conspiracy was hatched by Muslim accused, while the NIA later claimed right-wing extremists were behind the blasts.

"The case seems to have reached a dead end. The diagonally opposite stories in the chargesheet filed by the ATS and the NIA lead nowhere," said the HC order, made available on Thursday.

The ATS had collected incriminating material from the blast site, and forensic tests found RDX traces in soil samples from the explosion spot and from a godown linked to one of the nine accused, the court said.

"Both the samples were found to be the same," it noted.

For framing charges in grave offences such as murder, where punishment could extend to death, trial courts must carefully assess whether enough material exists to proceed, the HC said.

"The special judge overlooked the inherent contradiction and intrinsic improbability in the prosecution story as put forth by the NIA," it said.

The bench added there was no explanation for ignoring evidence collected earlier by the ATS and CBI.

"The things as stand today give two contradictory versions of the incident and both stories as floated by the ATS and NIA cannot be reconciled by any stretch of imagination," HC said.

The court stressed that evidence gathered by previous probe agencies still exists and must be considered by the special court.

"The trial court, while considering the question of framing the charges, has undoubted power to sift and weigh the evidence for the limited purpose of finding out whether a case is made out against the accused person," the judgment said.

According to the HC, the prosecution’s case against the four accused rests entirely on circumstantial evidence.

No eyewitness has testified to seeing them involved in the blasts, the court said, adding the NIA relied on retracted confessional statements and purported statements from another case.

"This is a mystery why the NIA did not collect fresh materials," it said.

The court also noted that the NIA’s revised theory was based on a statement by Swami Aseemanand, which was later retracted.

"The NIA has projected an entirely different story and states that the investigation of the case is still continuing and further evidence is being collected against the accused persons, and had requested the special court to permit it to continue further investigation of the case," HC said.

The alleged evidence that the appellants bought bicycles used in the blasts was hearsay, the court observed.

The NIA chargesheet had also named four wanted accused, two of whom were later shown as wanted in the 2008 Malegaon blast case.

Former BJP MP Sadhvi Pragya Singh Thakur, then Lt Col Prasad Purohit and five others were tried in the 2008 blast case. In July last year, a special court acquitted all seven for lack of evidence.

In the 2006 case, the NIA relied on Aseemanand’s statement claiming associates of deceased right-wing activist Sunil Joshi carried out the blasts. After he retracted the statement, the agency still filed a chargesheet giving a clean chit to the nine Muslim accused while naming the four discharged men.

A special court in 2016 discharged the nine Muslim men. The ATS challenged that order in the HC, where the appeal remains pending and unheard since 2019.

The HC had granted bail to the four present appellants in 2019, noting they had spent over six years in jail without trial.