At the centre of the Ishrat Jahan storm is an affidavit filed by the home ministry under P Chidambaram in which references to her alleged links with Lashkar-e-Toiba were deleted

Ishrat Jahan's death in a 2004 encounter is once again caught in a maze of allegations, counter-allegations and politics following ''revelations" by former home secretary GK Pillai and his erstwhile colleague RVS Mani.

At the centre of the storm is an affidavit filed by the Home Ministry under P Chidambaram in which references to Ishrat's alleged links with Lashkar-e-Taiba (LeT) were deleted.

This affidavit was in stark contrast to an affidavit filed earlier by the ministry in August 2009, where it had argued that Ishrat was an LeT operative and, thus, there was no need for a CBI probe into the encounter.

On 15 June, 2004, a special team of Gujarat police had killed Ishrat, a 19-year-old college student from Mumbra, along with Javed Shaikh alias Pranesh Pillai, and two alleged Pakistanis, Zeeshan Johar and Amjad Ali Rana, on the outskirts of Ahmedabad. Police said they were on their way to assassinate the then Gujarat CM Narendra Modi.

The case was handed over to the CBI after an investigation by a Special Investigation Team appointed by the Gujarat High Court said it was a fake encounter.

Pillai's story

Six years after retirement, a period during which he remained silent, Pillai has questioned Chidambaram's role in the alleged fake encounter of Ishrat Jahan. He has claimed that the home ministry deleted references to Ishrat's alleged links with the Lashkar-e-Taiba because Chidambaram did not want them to be a part of it.

According to Pillai, Chidambaram recalled the file from the joint secretary a month after the original affidavit — which described Ishrat and her slain aides as LeT operatives — was filed in the Gujarat HC.

"Mr Chidambaram, who was then the home minister, had asked for the file from the joint secretary, saying that the affidavit needed to be reworked. Only after the affidavit was revised, as directed by the minister, did the file come to me," Pillai told The Times of India.

Chidambaram, on his part, has claimed the revised affidavit was absolutely correct. The Congress has backed the former home minister, saying the BJP is trying to subvert a court-monitored investigation into Ishrat's alleged fake encounter. The Congress has hit back, saying Pillai now works for a corporate group with known affiliations.

Pillai has also argued that these four persons were lured into Gujarat as part of an intelligence operation. “It was a very successful intelligence operation… we managed to entice the LeT to send their shooters to India and were able to monitor their activities in India and to, in one sense, catch them… It was a very planned operation… something intelligence agencies around the world do.”

“Yes, it was a trap and it was a very successful operation… you are using the sources of LeT, people who think they are LeT, to be able to pass on information… It is always better to know when your enemy is coming in rather than wait for collateral intelligence where someone plans something without your knowledge," he said in the interview.

This gives credence to the theory that the Gujarat cops were waiting for Ishrat and the three men and to the rumours that Javed aka Pranesh was a double agent helping Indian intelligence agencies. Whether they were killed in retaliatory fire on the outskirts of Ahmedabad or were first captured, confined and then killed in cold blood, as several reports and enquiries have revealed, is now for the HC to decide.

Mani's affidavit

On Tuesday, RVS Mani, a former undersecretary in the home ministry told Times Now that he was coerced to file the second affidavit in the Ishrat Jahan case. The second affidavit is the one in which the references to the alleged links of Ishrat Jahan, Pranesh Pillai, Amjad Ali Rana and Zeeshan Johar with Lashkar-e-Taiba (LeT) were removed.

Before this, Mani, who was an undersecretary in the ministry's internal security department, had filed another affidavit claiming Ishrat and the three men killed in the encounter were LeT operatives. On the basis of this affidavit, filed in August 2009, the then UPA government had opposed a CBI investigation into the encounter.

But even the first affidavit filed by Mani is disputed. An audio tape of a purported conversation between PP Pandey and GL Singhal, two police officers accused of Ishrat's extra judicial killing, questioned the background of the first affidavit.

According to the Ahmedabad Mirror, the taped conversation was reportedly submitted by Singhal to the CBI during investigations into the encounter. 'The conversation between Singhal and Pandey indicates that these officers were not only aware of Mani’s arrival in the city to sign the affidavit, but they were also aware that advocate Abhichandani had been given the responsibility to vet the affidavit, the newspaper reported.

Interestingly, during the purported conversation, the two officers are heard discussing how the advocate vetting the affidavit can benefit if he "does it properly."

Here is the transcript of the purported conversation from the report:

GL Singhal: Sir, Namaskar.

PP Pandey: Are you in meeting?

Singhal: Yes Sir, Now I have come out.

Pandey: That order for Abhichandani is done?

Singhal: Ji, ji, Sir.

Pandey: Tomorrow, someone is coming. Undersecretary from Delhi, for signing affidavit.

Singhal: Right, right, Sir, right, Sir.

Pandey: Tell Abhichandani, if he does properly, we may try to make him High Court Judge.

Singhal: Right, right, Sir, will explain – Ji, ji Sir.

Incidentally, Mani had earlier complained that he was "coerced" by an officer of the SIT into signing a statement saying the first affidavit was drafted by two IB officers. According to the TOI, in his letter to the joint secretary in the urban development ministry, where he was posted then, Mani accused SK Verma, the SIT officer, of "coercing" him into signing a statement that is at odds with facts. "Knowing fully well that this would tantamount to falsely indicting of (sic) my seniors at the extant time, I declined to sign any statement," he had said then, the newspaper reported.

So, which affidavit was closer to the truth? Was Chidambaram trying to hide something in the second affidavit or just rectifying "errors" made in the first?

Ishrat's story is getting more complicated by the day.