[4] On April 13, the Crime Branch wing of state police took over the probe, and, on January 30, 1993, submitted a final report which tried to strengthen the suicide theory, with claims of psychological illness of the deceased.

In early November 2008, the HC handed over the case to the state unit of CBI, and gave a three-month period to complete the probe.

The new team, led by Dy SP Nandakumaran Nair, had recorded the statement of Sanju P Mathew, who had been residing next to the convent when Abhaya died.

Sanju, in his statement as per Section 164 of CrPC, said he had seen Kottoor in the convent hostel campus on the night of March 26, 1992, a day before Abhaya was found dead.

[4] On 22 December 2020, a special CBI court in Kerala's Thiruvananthapuram delivered its verdict in the 28-year-old murder case as it held Father Thomas Kottoor and Sister Sephy guilty.

The refrigerator door was left open, a bottle of water was spilt on the floor and a single slipper sat under the fridge – its pair was found beside the convent hostel's well.

A post-mortem conducted on the body by Dr Radhakrishnan of Kottayam Medical College found abrasions on the right shoulder and hip and two small lacerations above the right ear.

The series of inquiries by various investigating bodies that followed was lengthy, convoluted and unsatisfactory, plagued by internal conflict, bitter rivalries and allegations of corruption and bias, compounded by pressure from many quarters to bring the case to conclusion.

In April 1992 the Crime Branch of the Criminal Investigation Department took up the case, and months later ruled Sister Abhaya's death a suicide.

After years of failed investigations and internal struggles, two priests – Thomas Kottur, Jose Puthurukkayil and a nun – Sister Sephy – were arrested by the CBI under Nandan Kumar Nair on 19 November 2008.

[8][9] 67 nuns belonging to Abhaya's congregation petitioned the Chief Minister of the Kerala State Government to investigate the case as a homicide.

[10] On 27 March 1992, Kottayam West Police Station ASI V V Augustine visited the crime scene and called the fire force to search for Abhaya's body in the well in the compound.

[13] Some of the initial manipulations in the case by the local police and crime branch, alleged by CBI are: -The inquest report did not indicate the homicidal injuries on the body of Abhaya.

With this press conference, the case of Sr. Abhaya caught media attention all over India and the matter was strongly debated in the parliament as well as in the Kerala state assembly on several occasions.

Further on 3 June 1994 all the MP's from Kerala State jointly submitted a passionate petition to K. Vijaya Rama Rao, the Director of the CBI requesting him to disallow Thyagarajan to continue in the Abhaya's murder case.

Dr C Radhakrishnan, the forensic surgeon and former Principal of Kottayam Medical College, who conducted the post-mortem on the body of the deceased Abhaya, had given the report as death by drowning.

Graze abrasion 4 x 3 cm., oblique on the right side of the back of trunk, 9 cm below the lower end of shoulder blade with an upward and inward direction.

Pathak, the chief of the Forensic Department of Sawai Man Singh Medical college, Jaipur and Dr. Mahesh Varma, former chairperson of Anatomy Section submitted their formal expert report to the CBI investigation team to the effect that homicide could not be ruled out.

However, on 6 December 1996 the CBI filed a petition in the Chief Judicial Magistrate's court Ernakulam seeking to wind up its investigation in the matter for lack of evidence.

Justice Ramkumar of the Kerala High Court sent questionnaires to Dr. Malini, assistant director of the Bangalore centre where the narco analysis was conducted.

But Justice Hema, who heard the bail petition of the accused, based on Case Diaries, mentioned that the narco analysis CDs might have been manipulated and wanted the originals to be produced in court.

Others also alleged that due to the constant pressure that the action council and their convener and his secret financial backers that a lot of real good leads were never followed up on or investigated.

According to the CBI, their brain-mapping[clarification needed] and narco analysis investigations revealed that Abhaya woke up on 27 March 1992, early in the morning, descended the staircase and went to the hostel kitchen to get a drink of water from the refrigerator.

[28][29] On 1 January 2009, Kerala High Court Justice K. Hema granted conditional bail to Catholic priests Thomas Kootoor and Jose Puthrukakyil and Sister Sephy.

[35] Hema also mentioned the accusations propagated by the media, public and the CBI against officers of the local police and crime branch without any incriminating evidence.

[41][42] On 17 July 2009, the CBI DySP Nandakumar Nair filed a chargesheet in the Court of Chief Judicial Magistrate Ernakulam, charging Fathers Kottoor and Poothrikkayil and Sister Sephy with murder, destruction of evidence, and defamation.

[43] In September 2009, the tapes, which were claimed to be recordings of the narco tests conducted by CBI agents on the three accused were leaked to Kairali TV, a local television station.

In March 2018, Father Jose Poothrukkayil was acquitted by the special CBI court, which cited a failure on the part of the prosecutors to find substantial evidence that proves the accused visited the convent on the day of the murder.

This included hymen-restoration (hymenoplasty or hymenorrhaphy) procedure Sister Sephy underwent allegedly in the church's hospital, which was discovered through gynaecological tests conducted on her in late 2008.

The 1999 Malayalam film Crime File starring Suresh Gopi directed by K Madhu Nair in the lead role was inspired by Sister Abhaya's murder.