Nearly two decades after bombs tore through Malegaon killing 31 people, the Bombay High Court Wednesday quashed a special court’s order that had framed charges against the four men who were the last remaining accused in the case, effectively leaving one of Maharashtra’s deadliest terror attacks with no one to answer for it in court.

A bench of Chief Justice Shree Chandrashekhar and Justice Shyam C Chandak set aside a special court order from September 30, 2025, that had framed charges against Manohar Narwaria, Rajendra Chaudhary, Dhan Singh, and Lokesh Sharma for murder and criminal conspiracy under the Indian Penal Code, along with provisions of the Unlawful Activities (Prevention) Act, clearing the way for the trial. Their appeals against this order were allowed by the HC Wednesday.

The ruling ends, at least for now, the last active prosecution in a case that has passed through three investigating agencies, produced two contradictory theories about who was responsible, and hasn’t led to a single conviction in 19 years.

When bombs went off near a mosque and cemetery in Malegaon on September 8, 2006 claiming 31 lives and injuring 312 persons, Maharashtra’s Anti-Terrorism Squad moved quickly and arrested nine Muslim men. The CBI, which took over in 2007, kept the same accused. But when the National Investigation Agency (NIA) stepped in four years later, it reversed the entire theory of the case, declaring the nine Muslim men innocent and pointing instead at a network of Hindu right-wing activists.

The pivot rested heavily on a statement made in December 2010 by Swami Aseemanand, who was already in custody for other blast cases and had claimed that activist Sunil Joshi had told him the 2006 Malegaon bombing was carried out by “his boys.” The NIA used this to build a new chargesheet naming the four appellants, along with the deceased Joshi and three others still at large.

But Aseemanand soon retracted the statement, claiming it was extracted under torture. And crucially, courts trying him in the Samjhauta Express, Mecca Masjid, and Ajmer Sharif blast cases had all rejected that confession as unreliable, acquitting him each time.

The four men’s lawyer, Advocate Kaushik Mhatre, argued before the Bombay High Court in January that there was no eyewitness against his clients, and that a confession no other court had believed could not be the basis for framing charges. The HC found a “prima facie case for interference” and stayed the trial pending its final order, which came on Wednesday.

Appellants Narwaria, Chaudhary, Singh, and Sharma were arrested in 2013 and spent six years in prison before the HC granted them bail in 2019, observing pointedly that they had been incarcerated without trial for over six years.

Meanwhile, the nine Muslim men originally arrested were discharged in 2016, but the ATS challenged that discharge in the HC. That challenge has not been heard since 2019 and remains pending.

Wednesday’s ruling leaves the 2006 Malegaon blast case in a peculiar situation in which the original accused have been discharged and the replacement accused now have their charges quashed.

The verdict lands less than a year after a special NIA court acquitted all seven accused in the separate 2008 Malegaon blast case, including former BJP MP Sadhvi Pragya Singh Thakur and Lt Col Prasad Purohit, citing insufficient evidence.