Mumbai | The 2006 Malegaon blasts case "seems to have reached a dead end," the Bombay High Court said while discharging four accused and pulling up the National Investigation Agency (NIA) for "completely ignoring" incriminating evidence collected by previous probing agencies.

The high court's order, which was passed on Wednesday and made available on Thursday, leaves unanswered the significant question of who was responsible for the September 8, 2006, explosions that claimed 31 lives and injured 312 others.

A division bench of Chief Justice Shree Chandrashekhar and Justice Shyam Chandak quashed a September 2025 special court order that had framed charges against Rajendra Chaudhary, Dhan Singh, Manohar Ram Singh Narwaria, and Lokesh Sharma.

"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 bench said that the special judge had not "applied his mind" and overlooked the "inherent contradiction and intrinsic improbability" of the NIA's prosecution story, which relied on retracted confessions and circumstantial hearsay rather than fresh material.

In reaching to this conclusion, the high court anchored its judgment in legal principles established during the pre-Independence era, citing rulings from 1914 and 1934.

The bench referenced Lord Sumner's 1914 judgment (Ibrahim versus The King), which established the "positive rule" that no statement by an accused is admissible unless proven voluntary and not obtained through fear or hope of advantage.

The court also cited Lord Russell of Killowen's 1934 ruling (Sheo Swarup versus King Emperor), emphasising that an appellate court must not be burdened by the trial court's opinion but must independently review the weight and reliability of all evidence.

The high court said the NIA's probe "completely ignored" the initial probe by the Maharashtra Anti-Terrorism Squad (ATS), which provided a "vivid narration" involving nine Muslim men arrested earlier in the case.

The court highlighted that the ATS had collected forensic evidence showing matching RDX traces from the blast site and a godown belonging to one of the initial accused.

"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," the court said.

While the ATS and the CBI initially pointed to an organised crime syndicate, the NIA later projected an entirely different story alleging right-wing extremism based on a statement by Swami Aseemanand, which he later retracted.

Relying on a 1973 Supreme Court judgment, the bench reminded the prosecution that "a criminal trial is not like a fairy tale wherein one is free to give flight to one's imagination and fantasy".

Noting that the four appellants had already been incarcerated for over six years without trial before receiving bail in 2019, the high court concluded that there was insufficient evidence to justify proceeding with the trial against them.

They were charged under the Indian Penal Code (IPC) sections for murder and criminal conspiracy, and the Unlawful (Activities) Prevention Act (UAPA), a stringent anti-terror law.

On September 8, 2006, four bombs exploded at Malegaon town in Maharashtra's Nashik district, three inside the premises of Hamidia Masjid and Bada Kabrastan just after Friday prayers, and the fourth in Mushawarat Chowk, killing 31 persons and injuring 312 others.

The HC said the NIA's case against the four accused solely rests on circumstantial evidence.

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

A special court in 2016 discharged the nine Muslim men, which the ATS challenged in the HC. Its appeal is pending and has not been heard since 2019.

The HC in 2019 granted bail to the four present appellants, observing they had been incarcerated for over six years without trial.