Subversion has its boundaries. Not though apparently in India during a critical period between 2008 and 2014. Let's examine how investigations by the Central Bureau of Investigation (CBI) and the Special Investigation Team (SIT) into the terror attack on the Samjhauta Express and the gunning down of Ishrat Jahan were subverted - and by whom.

First, the Samjhauta Express. As India Today's story uncovered last week, the investigation into the Samjhauta terror strike was turned on its head. On July 1, 2009, the United States treasury and the United Nations Security Council (UNSC) named Arif Qasmani as the principal accused in the Samjhauta attack. Both concluded the terror strike originated in Pakistan. The UNSC placed a travel ban on Qasmani and froze his assets.

The Maharashtra Anti-Terrorism Squad (ATS) and the CBI ignored the UNSC's findings. Instead, it blamed fringe right wing Hindu groups for the attack.

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Meanwhile, colonel Prasad Shrikant Purohit, allegedly a part of a fringe Hindu group, was arrested in November 2008 in the Malegaon blast case. He has been in jail for nearly eight years. No charge sheet has been filed. Sadhvi Pragya Thakur, another accused, has been in jail for over seven years without a charge sheet.

The ATS and CBI used these arrests to construct a narrative of "Hindu terror" that played through the May 2009 Lok Sabha election. The CBI and ATS wilfully ignored advice from US authorities that Pakistan-based terrorists were responsible for the Samjhauta Express blast. They also ignored the UNSC's conclusion naming Qasmani as the principal accused in the Samjhauta case. Instead, they arrested a clutch of Hindu right wing groups.

This narrative has now been turned upside down. Dozens of witnesses in the Samjhauta blast have turned hostile. Let's focus on two of the most important. The first is Dr RP Singh, an endocrinologist. He had initially told the Maharashtra ATS that he attended meetings when plots to "avenge jihadi terror attacks" were discussed by Purohit, Pragya Thakur, Aseemanand and others.

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Dr Singh says he was tortured by the Maharahstra ATS to make the statement framing the accused. Here's what Dr Singh, consulting endocrinologist with a well-known private hospital, testified on April 6, 2016, before a judicial magistrate: "I was tortured by Maharashtra ATS to give a statement earlier against Abhinav Bharat and its members."

To back his claim that he was not present at the meeting as alleged by the ATS, Dr Singh produced authenticated travel documents and witnesses to prove that he was elsewhere on the relevant day and had not travelled to Bhopal or Nashik where the "Hindu terror" meetings took place.

The second key witness among the 40-odd witnesses who have turned hostile is Yashpal Bhadana. He too has claimed he was coerced by the ATS into making an incriminating statement against the accused. Both Dr Singh and Bhadana have recorded affidavits in front of a judicial magistrate under Section 164 of the CrPC, retracting their earlier statements made to the Maharashtra ATS allegedly under duress and stating under oath the facts of the case.

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Who were the real perpetrators of the Samjhauta blast? The trail leads directly to Pakistan. According to the US and UNSC findings, Qasmani is the principal accused in the Samjhauta blast. Operatives of the banned Students Islamic Movement of India (SIMI) and the Indian Mujahideen (IM) were trained in Pakistan. They received explosives and detailed instructions in Pakistan just before the attack.

Yet the ATS and CBI ignored all this evidence. Instead, they allegedly coerced witnesses like Dr Singh and Bhadana to implicate Pragya Thakur and others to develop a narrative of "Hindu terror".

Rahul Gandhi adopted this narrative when he told a United States envoy, according to WikiLeaks (a report not explicitly denied by Rahul), that "saffron terror" was more dangerous to India than Islamist terror.

That narrative has come to an abrupt end with the latest revelations. The Maharashtra ATS stands discredited. The CBI has lived up to its reputation as a caged parrot. The National Investigation Agency (NIA) must now take the 2007 Samjhauta case to its logical conclusion. The director-general of the NIA, Sharad Kumar, has promised to file a final report on the Samjhauta case in the next six weeks.

Ishrat Jahan

Meanwhile, the Ishrat Jahan case has got murkier. It has striking similarities to the Samjhauta case. Here too the evidence was seemingly subverted. The opinions of three credible officials in the UPA government and three key organisations were ignored.

The former national security adviser (NSA) MK Narayanan wrote an article in The Hindu on February 18, 2016. The article indicated that Ishrat was an LeT terrorist, who was killed in a controlled counterterrorism operation along with two Pakistani nationals (Zeeshan Johar and Amjad Ali) and an Indian (Javed Sheikh) who had made several trips to Pakistan.

Ishrat Jahan.

Narayanan's view on Ishrat's LeT links as well as the nature of the encounter was echoed by former home secretary GK Pillai and former Intelligence Bureau (IB) chief Asif Ibrahim. Both indicated that it was a legitimate counterterrorism operation.

During the politically malignant period of 2008-14, the narrative on Ishrat was reflected in the two infamously contradictory affidavits dated August 6, 2009, and September 30, 2009. Both bear then home minister P Chidambaram's signature. He has now denied that he signed either affidavit.

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The CBI and the court-appointed SIT once again ignored written evidence from the US Federal Bureau of Investigation (FBI), the NIA and the legal attaché in the Indian embassy in the US that a) Ishrat was an LeT terrorist and b) her module was planning an imminent attack on a top political leader in Gujarat.

All this evidence was dismissed as hearsay by the SIT and CBI. Using third-degree methods on home ministry and IB officials like RVS Mani and Rajinder Kumar in order to force them to toe the "Ishrat-as-innocent-college-girl" line, the SIT allegedly subverted the investigation and misled the court.

What now? The NIA must complete its investigation, file its final report and present the true facts to the Gujarat High Court where the Ishrat case is being heard. The court will then be able to pass judgment based on all, not some, of the facts.

Congress defence

Congress leaders point out that the Ahmedabad Metropolitan Court in 2009 held that Ishrat was killed in a fake encounter. The CBI charge sheet in 2011 said the same. The SIT appointed by the Gujarat High Court arrived at the same conclusion.

As has now emerged, the CBI and SIT presented incomplete and misleading evidence to the metropolitan court. The FBI, NIA and the US legal attaché's written evidence that Ishrat was part of an LeT terror module planning an imminent political assassination in Gujarat was dismissed by both the CBI and SIT in 2011 and 2013.

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In doing so, they followed the exact pattern of the Pakistani investigation into the 26/11 Mumbai terror attack. The Pakistani special court was given incomplete and misleading evidence against Zaki-ur-Rehman Lakhvi and Hafiz Saeed. The 26/11 case, as a result, is now virtually dead. Courts can only pass judgment based on the evidence presented to them.

In both the Samjhauta and Ishrat cases, the CBI and SIT in 2013 did precisely what their Pakistani counterparts have done since 2008 to stall the 26/11 trial. That is a severe and telling indictment.