In a span of 10 days, the Maharashtra Anti-Terrorism Squad (ATS) and National Investigation Agency (NIA) have received major blows in two big terrorism cases, with courts junking their investigation and finding no substance in their theories, leading to the accused being let off.

Pointing to lapses in the Malegaon investigation, the Special NIA Court Thursday said: “Though there was strong suspicion against the accused persons, the investigating agencies failed to establish their guilt beyond reasonable doubt to convict them.”

The September 2008 Malegaon blasts had left six people dead and over a hundred injured. All the seven accused, including former BJP MP Sadhvi Pragya Singh Thakur, were acquitted by the court Thursday.

The ATS’s case was that the blasts were carried out by people with radical Hindutva leanings, with the communally sensitive Malegaon chosen deliberately for an attack during the month of Ramzan and on the eve of Navaratri.

On July 21, the Bombay High Court set aside a special court verdict, acquitting all 12 accused in the 2006 Mumbai train blasts case that killed 186. Of the accused, five had been awarded death sentences and seven life terms.

Both these cases happened under Congress-led governments in the state and at the Centre — and were first investigated by the state ATS. Both had communal and political overtones; hence, amid allegations from political parties, different probe agencies were roped in at different stages of the case, impacting the overall investigation.

In the Mumbai train blasts case, the ATS built a case blaming individuals linked to members of the Students’ Islamic Movement of India, backed by Pakistani terror outfit Lashkar-e-Taiba (LeT). The Special MCOCA Court validated the ATS’s investigation and, in October 2015, awarded the death penalty to five of the convicts and life terms to seven others.

The accused kept claiming that they were subjected to torture during the custodial interrogation.

On July 21, the Bombay High Court set aside this verdict, putting a big question mark on the ATS’s theory that individuals linked to SIMI had orchestrated the blasts.

This is important as, two years after the train blasts, the Mumbai Crime Branch, then headed by Joint Commissioner of Police Rakesh Maria, had claimed that when they busted the Indian Mujahideen (IM) module that had carried out blasts in Ahmedabad and other parts of the country, their members had admitted to also having carried out the Mumbai train blasts.

In the Malegaon case, in October-November 2008, the ATS under its then chief Hemant Karkare made arrests of several alleged Hindu fundamentalists, including Thakur, and invoked MCOCA.

However, soon after, Karkare was killed during the November 26, 2008, Mumbai attack, after which former ATS chief K P Raghuvanshi was roped in to investigate the Malegaon case. He was first given additional charge of the ATS for seven months, then made full-fledged ATS chief and promoted to ADG rank.

During his first stint with the ATS, Raghuvanshi, incidentally, had led the investigation into the 2006 Mumbai train blasts as well.

Karkare’s investigation, alleging the involvement of Hindu extremists, was reflected in the first chargesheet filed by the ATS in January 2009, followed by a supplementary chargesheet in April 2011.

However, in April 2011, the Ministry of Home Affairs, under the UPA government, suo motu directed the NIA to take up further investigation. The Central agency registered cases under provisions of the MCOCA, UAPA, Explosive Substances Act, and Indian Penal Code.

In May 2014, the UPA was replaced by the BJP-led NDA at the Centre. Two years later, on May 13, 2016, the NIA filed its second supplementary chargesheet in the case, which dropped MCOCA charges against all the accused.

This was significant as the ATS had relied heavily on confessional statements made by some of the accused, which were admissible as evidence under MCOCA.

After the NIA took over, 33 witnesses turned hostile in the case. Some claimed that their accounts were recorded under pressure.

Before the trial could commence in the case, the NIA moved court requesting that Pragya Thakur be dropped as an accused as there was no witness or proof to show she was involved in the conspiracy. However, the court did not accept this, citing the prima facie evidence against her.

In May 2015, Special Public Prosecutor in the case Rohini Salian told The Indian Express that NIA officers had put pressure on her to “go soft” on the accused and not to appear in hearings.

Calling the ATS investigation into the Malegaon 2008 blasts flawed, former Additional DGP P K Jain said that 33 witnesses turning hostile in one case was very unusual, and indicated major flaws in the investigation. The Nashik Range IG when blasts hit Malegaon in 2006, Jain said the initial police investigation then had found the role of local persons and two Pakistanis.

But the ATS, while probing the 2008 Malegaon blasts, blamed alleged Hindu fundamentalists for the 2006 blasts too, Jain said. The original accused were discharged and a new set of accused were injected, thus ruining the whole case, he alleged.

After the Central and state governments came under criticism for failing to provide justice to the victims of the train blasts case, the Maharashtra government had promptly challenged the verdict in the Supreme Court of India.

It is to be seen if the NIA challenges Thursday’s verdict in the High Court.