On the morning of March 27th, 1992, 21-year-old nun Sister Abhaya, a student of Kottayam's BCM College, and a member of the Knanaya Catholic community was brutally murdered. Since then, her death was initially registered by the state police and crime branch as suicide, until the CBI later concluded that it was murder. In 2009, the CBI charge-sheeted Catholic priest Thomas Kottoor and Sister Sephy in the case.
At the time of her death, Abhaya had been a pre-degree student in college run by the Catholic Church. She had been an inmate of Pious Xth Convent Hostel, which had 123 inmates, including 20 nuns, in 1992 when the incident happened. On the fateful morning of her death at around 4 am, sister Abhaya came down the hostel steps to fetch herself a bottle of water. Upon entering the kitchen, she finds father Kottoor and Sister Sephy in a compromising position. Before she could flee, reports claim that Kottoor held her down and covered her mouth, while sister Sephy hit her on the head with an axe, leaving her unconscious. As per police reports, sister Abhaya was last known to have gone to the kitchen for a drink. The refrigerator door was left ajar, 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. After a brief search, her body was found in the convent hostel's well in the early hours of the same day.
In the first of its three reports in the case, the CBI said the nun's death was a case of "homicidal suicide". But the CBI court rejected the report and ordered a fresh investigation. In its second report, the agency said it could not establish beyond doubt whether it was a suicide or murder.
In its last report filed in 2008, the CBI said it was a case of murder and arrested Kottoor, Jose Poothrukayil, (another priest) and Sefi. On 22nd December 2020, after 28 years of investigation, the CBI Court found Father Kottoor and Sister Sephy to be guilty of the murder. The verdict is attributed to the key witness, Adakka Raju who stumbled upon the scene of murder while on a robbery. The witness' evidence proved crucial in the trial as the many of other witnesses reneged on their testimony and he was the only one who did not surrender to the threats and bribes. On the historic day of 23 December 2020, CBI court sentenced both to life imprisonment and imposed a fine of 5 lakh each.