The CBI officer Nandakumaran Nair, who took over the investigation of the death of Sister Abhaya in November 2008 and in quick time recorded the arrest of the prime accused, described the case as one of “sex and murder” while deposing before for the CBI Special Court in Thiruvananthapuram on Tuesday.

On the other hand, while cross-examining the CBI officer, the defence team led by senior counsel Raman Pillai sought to discredit his track record and demonstrate that the officer had invented lies to frame the accused.

Nandakumaran Nair, now the CBI Superintendent of Police in charge of Kerala, said he had found the two main accused, Fr Thomas Kottoor and Fr Jose Puthrikayil, “deceptive” the first time he questioned them. “And they made contradictory statements,” the CBI officer said.

As for Sister Sephy, the third accused, Nandakumaran said she refused to cooperate. “All our attempts to make her talk were in vain,” he said.

A farce of an investigation

Nandakumaran Nair, who took over the investigation as a young CBI deputy superintendent of police, said the earlier police investigation was riddled with mistakes. “Fingerprints were not taken from the scene of crime,” he said. “The inquest report was also found to be fabricated. The veil and slippers (of Sister Abhaya) were not subjected to forensic tests and the material objects recovered from the scene of crime were destroyed,” he said.

Further, the CBI officer said the Crime Branch had not even returned the material objects (a nun's veil, a brown plastic slipper and a water bottle) to the Sub-Divisional Magistrate's office, Kottayam.

His investigation had also ruled out the possibility of the contusion on Sister Abhaya's head being caused by an iron pipe deep under the well in which her body was found. The police version was that the nun had committed suicide by jumping into the well, and in the process had hit her head on one of the pipes below.

He said the Crime Branch version was “devoid of reason and logic”. He said the contusion on top of Sister Abhaya's head was caused by the “blunt metal edge” of a handaxe.

Ban on lie-detector truths

Senior defence counsel Raman Pillai, however, did not allow Nandakumaran Nair to dwell on the evidence he had deduced from polygraph tests, brain mapping and narco analysis done on the accused to substantiate his findings. Raman Pillai insisted that the Supreme Court had made it clear that such tests were inadmissible as evidence in a court of law.

Even as Raman Pillai kept objecting, Nandakumaran Nair told the Court that the CBI team led by him had followed all protocols and secured all permissions, including that of the accused and the courts, before conducting such deception-detection tests. Yet, he was not allowed to elaborate.

Cracks in the President's medal?

Raman Pillai's strategy was to question the professional credibility of the CBI in general and Nandakumaran Nair in particular. “Has not the High Court made serious and adverse remarks against the CBI when the case was handed over to a team led by you,” Raman Pillai asked.

“Some observations were made in the interest of the investigation,” the CBI officer said. The High Court had in 2008 asked why a junior officer like Nandakumaran Nair was asked to helm the investigation.

Pillai then quoted from another Court order, regarding a bail application moved in connection with a case concerned with the suicide of CBI additional SP Haridutt, in which it is said that Nandakumaran Nair should be “disciplined and bridled”.

Nair said the observation was made without hearing his side, and later when he got an occasion to speak on his behalf, the officer said the High Court had quashed a writ petition against him. The CBI officer also used the occasion to remind the defence team that he was an officer who had received the President's medal for meritorious service.

Thief as the only ally

Nonetheless, the CBI officer found himself in a spot of trouble when he told the court that the main accused, Thomas Kottoor and Jose Puthrikayil, used to enter the St Pius Convent during “unearthly hours in a hush-hush and secretive manner”.

Raman Pillai asked him whether he was able to find a single witness within the convent who had seen the accused sneaking into the Convent in a “secretive” manner. He did not. “It was done so secretively that no one inside the Convent had seen them,” the CBI officer said. Raman Pillai smiled.

The senior defence counsel then said this proved that the CBI officer knew that his clients had not entered the Convent the way he had described. “You were only inventing lies,” he said.

The CBI officer said it was not a lie and told the Court that Adaykka Raju (a thief and a prosecution witness) had seen Kottoor and Puthrikayil furtively entering the convent in the dead of the night.

(Adaykka Raju had given the statement in the CBI Court that he had seen the two accused while he was trying to steal the copper strips of the lightning rod installed on the terrace of the Convent.)

Raman Pillai then asked Nandakumaran Nair to show whether Adaykka Raju's name was mentioned in the chargesheet of R K Agarwal, the CBI officer in charge before Nair took over. There was none. The thief's name figured only after Nair took over. Clearly, the defence argument is that Adaykka Raju was a witness manufactured later by the CBI, perhaps using a bit of third degree. (Raju himself had spoken of CBI torture.)

Vanishing witnesses

Another 'outside witness', a neighbour named Sanju P Mathew who had initially said he had seen Kottoor's scooter outside the Convent's wall on the night of Sister Abhaya's death, had turned hostile in 2019. A third witness, the night security of a building close to the convent named Chellamma Das, died in 2014.

Now, there is virtually no one who had seen the main accused entering the Convent on March 27, 1997, the day 18-year-old Sister Abhaya was found dead.

Nandakumaran Nair's cross-examination will continue on Wednesday.