Sister Abhaya murder case

The Sister Abhaya Case is a case regarding the death of a Knanaya Roman Catholic nun, who was found dead in a water well in St Pius X convent in Kottayam, India, on 27 March 1992. She was 19 years old at the time of her death and was a member of St. Joseph's Congregation for women under the Knanaya Catholic diocese of Kottayam, Kerala in India. She was a pre-degree student of BCM College, Kottayam and was staying in St Pius X Convent/Hostel at the time of her death. On the day of her death she got up from sleep early at around 4 am to study for her exam, had gone down to the kitchen of the hostel to get water from the refrigerator. Later her body was found in the well outside the kitchen in the convent/hostel compound.
In October 2009, Sister Abhaya's father wrote letters to the Chief Justice of India and President of India alleging that Justice Cyriac Joseph of the Supreme Court was trying to destroy evidence relating to the case.
Initially the local police crime branch concluded that the death was a result of suicide. Protests by the action council and a petition by the nuns of the congregation led to reinvestigation by the Central Bureau of Investigation (CBI). Though CBI concluded that Abhaya was murdered, they requested closure of the case for want of evidence. The request for closure was rejected by the courts. It was only after 16 years that they made the first arrests in the case. On 19 November 2008, two priests of the Kottayam Knanaya Catholic Diocese and a nun were arrested by the CBI.http://www.hindu.com/2008/11/20/stories/2008112050270100.htm These arrests are considered as part of conclusions to a 16-year-old unresolved case.http://in.youtube.com/watch?v=2EaopvI7eM0
The case assumes importance in India's judicial and law enforcement history on various counts. It has been investigated and reinvestigated by various police agencies of Kerala and various teams within Central Bureau of Investigation (CBI-India) for 16 long years. Manipulations by police, forensic teams and medico legal experts were alleged. Interference in the investigation by senior police officers and by politicians, was also alleged. There was also allegation of trial by the media. The Catholic Church in Kerala also was on the defence on allegations of murder and sexual misconduct by its priests and nuns. The Kerala Police, Kerala Crime Branch and CBI have been in the dock for inefficient, tardy and ineffective investigations and for allowing undue bureaucratic and political interference in the investigations.
The case is also a typical example of judicial activism, with the Court refusing to accept police closure reports and ordering reinvestigation of the case again and again. The case also stands out for social activism, for the role played by the Civic Action Council to doggedly pursue impartial investigation in the case. Social activist Jomon Puthenpurackal pursued the case for 16 long years but he has been the target of various allegations on his motives. The high court has ordered a police investigation of Jomon including his financial affairs. This was challenged by Jomon in the Supreme Court, but the Supreme Court refused to stay the investigation. The parents of Sr. Abhaya has alleged profiteering by Jomon and has disassociated themselves from the action council. Allegations have been made that the investigations in the case were stalled and evidence destroyed as a result of powerful influences exerted by those involved as accused in the case.
This is also a case where scientific investigation methods such as polygraph tests, brain mapping/brain fingerprinting and narco analysis were used to solve the case. The Supreme Court is to decide whether the tests are a violation of human rights and personal liberty. The narco test CDs were leaked to the media, some of who transmitted the same with slanted commentary against the accused, against court orders. This has been challenged in the courts as a naked violation of human rights.
== Time lines ==
* March 1992 around 4:00 AM: Abhaya gets up from sleep to study for exam. Goes to the kitchen to get water from the fridge.
*A search at dawn finds her body in the well in the compound.
* March 1992: FIR is registered as missing person case and later as unnatural death by Kottayam West Police Station
* March 1992 10 AM: Abhaya's body is taken out of the well by Firefighters and inquest drawn up
* March 1992: Post-mortem conducted on the body by Dr Radhakrishnan of Kottayam Medical College
* March 1992: Action Council convened by Jomon Puthenpurackal 
* April 1992: Crime Branch takes up investigation
* January 1993: Crime Branch files closure report as death by suicide
* March 1993: CBI (Varghese P. Thomas) takes up investigation on orders of Central Government (CBI Headquarters) on the request of the State Government 
*April 1993: Material objects in the case received from the RDO court and destroyed by the Crime Branch.. 
*30 December 1993: Varghese P. Thomas, DSP, CBI submits resignation alleging illegal interference in the investigation by V Thiagarajan, SP, CBI, Cochin.
*7 April 1995: Dummy experiment conducted. Forensic medical experts (Dr S K Pathak, Dr Mahesh Verma, Dr. S R Singh) conclude that homicide cannot be ruled out.
*29 January 1996: CBI SP Ohri submits final report. Suicide or murder cannot be conclusively proved. CJM court rejects report. CBI to continue investigation.
*9 July 1999: DySP Surinder Paul submits report. Homicide, but unable to find culprits. Report again rejected by CJM court.
November 2007: Fr. Kottoor, Fr. Puthrukayil, Sr Sephi, Sanju P Mathew etc. undergo narco analysis tests in Bangalore.
*7 November 2008: High Court orders investigation by Kerla unit of CBI.
*19 November 2008: Two priests and a nun arrested in the case by a CBI team led by Nandakumar Nair, DySP, CBI, Cochin.
*25 November 2008: V V Augustine, former ASI who registered the FIR and conducted inquest on the dead body, found dead (committed suicide). Suicide note alleges torture by CBI.
*2 December 2008: Accused remanded to police custody by CJM.
*29 December 2008: Bail application rejected by the CJM Ernakulam. Bail applications before Justice Ms. Hema of High Court. She says arguments of CBI counsel contrary to the facts recorded in the case diary. CBI requests for transfer of case. Rejected by High Court.
Controversial editorial by Kerala Kaumudi.
*2 January 2009: Justice Ms. Hema of Kerala High Court grants conditional bail to the three accused. Suspects manipulations in Narco CDs. Orders production of originals. CBI moves Single Bench of Justice Basanth saying case paralysed by the orders of Justice Hema. Basanth orders only he can monitor the case.
Basanth's orders refuted by Hema the next day. Says all High Court judges are equal. Only a superior bench can change her orders.
Controversy among the media, bar and public about the open disagreements among the two judges.
Justice Basanth recuses himself from monitoring the case.
* 14 January 2009: Supervision of the case transferred to a Division Bench of the Kerala High Court.
Originals of the Narco CDs placed before the CJM court. Orders verification by CDAC.
*20 February 2009: Jomon's autobiography titled Abhaya case diary released.http://www.expressbuzz.com/edition/story.aspx?Title=VS+has+no+fighting+spirit+now,+says+P+C+George&artid=WyoJvH0HB4I=&SectionID=lMx/b5mt1kU=&MainSectionID=lMx/b5mt1kU=&SEO=K+E+Mammen,+D+Sreedevi;+Chief+Minister;+V+S+Achuth&SectionName=tm2kh5uDhixGlQvAG42A/07OVZOOEmts
*9 March 2009: CDAC returns Narco CDs citing technical inability to verify the CDs. CDIT to verify CDs. 
*12 March 2009: Bail conditions of all the accused relaxed by high court. High court closes all the proceedings regarding Abhaya case before it. CJM court Ernakulam to continue proceedings.
CBI requests CJM court to sanction narco analysis test to be conducted on Abhaya's roommate Sr. Sherly and two kitchen servants. Court gives sanction. Sanction challenged in High Court.
*23 March 2009: Kerala Kaumudi submits unconditional apology. High Court closes contempt case.
*20 June 2009: CDIT finding that Narco CDs doctored. Court orders CBI to find out original CDs/tapes.
*4 July 2009: CBI questions Dr. Malini and others.
*& July 2009: CBI makes a volte face and submits that the CDs were not doctored. CDIT challenges the CBI findings.
*15 July 2009: Justice Hema while relaxing the bail conditions of Fr. Puthrukayil observes that collusion between CBI and Dr. Malini proved by latest events.
*17 Jul 2009: The CBI, Kochi Branch filed chargesheet in the Court of Chief Judicial Magistrate, Ernakulam against two priests and a nun. 
* 24 July 2009: Abhaya"s father files contempt of court petition against CBI for failure to produce original narco CDs.
*30 July 2009: Justice Hema again criticises CBI. Orders production of charge sheet.
* 3 August 2009: A division bench of high court consisting Balakrishnan Nair and Ravikumar to hear all petitions in Abhaya case. bail conditions of Sr. Stephy relaxed.
* 5 August 2009: Supreme Court refuses CBI plea to stay the contempt of court proceedings in high court.
* 7 August 2009: Stung by repeated criticism in high court, CBI replaces counsel Namboodiri with Sreekumar.
* 12 August 2009: Supreme court stays CJM and High court orders which allowed CBI to conduct narco tests on a nun and two maids who were inmates of Pius IX hostel at the time of Abhay's death.
* September 2009: CBI files charge sheet against the three accused. Edited CDs of narco tests transmitted on TV channels on the same day. CJM court orders channels to stop the transmission of the CDs. Accused files contempt of court petitions against the TV channels.CBI files chargesheet in the Sister abhaya murder case Press Release - CBI
* December 2009: Supreme Court rejects Jomon"s plea to stay the investigation ordered by high court regarding his financial and other deals.
== Action council ==
An Action Council was convened by Jomon Puthenpurackal on 31 March 1992 and sent a plea to all concerned - the Chief Minister of the state, the Prime Minister, the President, the Chief Justice of the High Court of Kerala, the Director General of Police and so on - demanding prosecution of the culprits for the murder of Abhaya. The local police who first investigated the matter could not bring out any evidence to prove murder. The Action Council had also to face allegations that the Action Council was more of a witch-hunt spearheaded by Jomon and his financial backers to promote their own agenda. 
67 nuns belonging to Sr. Abhaya"s congregation led by the superior of the convent, petitioned the Kerala State Government that the case should be investigated as homicide. The Director General of Police of Kerala on 7 April 1992 directed the Crime Branch section of the [Kerala Police to take up the investigation from the local police. The Crime Branch led by KT Michael, SP and Kunju Moideenkutty, DySP/SP, after their investigations submitted their report before the Sub-Divisional Magistrate (RDO) on 30 January 1993, according to which Abhaya had committed suicide. 
The Kerala Government, on the basis of the petition by the nuns belonging to Abhaya's congregation, recommended a CBI enquiry to the Central Government. Accordingly, on 29 March 1993, CBI took up re-investigation of the case. Varghese P Thomas, Dy SP was the Chief Investigating Officer.
== Various investigations ==
=== Kerala Police ===
The FIR in the case was registered by Kottayam West Police Station ASI V V Augustine on 27 March 1992 as a missing person case and later as unnatural death. The ASI visited the crime scene and called the fire force to search for the body in the well in the compound. The Fireforce took out the body of Abhaya from the well in the compound of St. Pius X Convent. An inquest was prepared by ASI Augustine. Photographs of the body were also taken.
Clothings of Abhaya and other material objects such as slippers were taken into custody and sent to the RDO's court. Later these items of physical evidence were destroyed on a petition filed by the crime branch stating that Abhaya had committed suicide.
The body was sent for post-mortem. The post-mortem report indicated death by drowning. The post-mortem also had reported homicidal injuries on the body, including injuries on the head.
ASI Augustine was found dead on 25 November 2008, and had committed suicide alleging torture by CBI.
Initially, the local police investigated the case and reported as suicide. 
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.
-The material evidence in the case was destroyed and the clothes were not subject to forensic examination
-The photographs showing injuries on the body were removed.''
-The crime scene was tampered with or material physical evidence was not collected from the crime scene. 
During the initial inquiry, the post-mortem, chemical examination and laboratory report also had been erased and then rewritten due to other influence.
=== Crime branch ===
On 7 April 1992, the Director General of Police of Kerala directed the Crime Branch section of the Kerala police to take up the investigation. The Crime Branch submitted its report before the Revenue Divisional Officer (RDO) on 30 January 1993. As per the report, the Crime Branch had reached the conclusion that Abhaya had committed suicide. According to the post mortem report, she had died from drowning. Though there were allegations that the Crime Branch had procured the material objects in the case from the court and destroyed them, this has been disproven by the CBI themselves later on. The final report submitted by DySP Surinder Paul of the CBI Delhi Unit:"No viscera of the deceased was deposited by any police officer in this case” (Page 14, Para 20). As part of the normal process followed by courts in case of un-natural deaths, a court employee issued a note on 07/06/1993 for the destruction of the viscera and on approval from the Sub-Divisional Magistrate, the materials were destroyed.
The report says “…that the orders for disposal of case property of this case were given in a routine manner/practice without any specific interest for disposal of Case Property” (Page 13, Para 19. Final Report by Surinder Paul dated. 09.07.99)
This was almost 2 months after the CBI first took over the case. This points to the negligence on CBI's part and later alleging that Crime Branch had destroyed the evidences.
=== CBI ===
The Central Bureau of Investigation (CBI), India's premier investigating agency, started investigating the death of Sister Abhaya on 29 March 1993, under the direct supervision of its officer Varghese P. Thomas. He was then serving as deputy superintendent (DSP) of CBI.
=== DySP’s controversial resignation ===
On 30 December 1993, Varghese P. Thomas resigned from the service of CBI and from the investigation of Abhaya's death. He had seven more years in service to retire. He had arrived at the conclusion that Abhaya's death was a case of murder and he had recorded it as such in the Case Diary. Subsequently, on 19 January 1994, he called a special press conference in Cochin and announced that he had resigned from CBI as his conscience did not permit him to comply with a strong directive given by his superior officer, V. Thyagarajan, the then Superintendent of CBI Cochin Unit, who had asked Varghese P. Thomas to record the death of Abhaya as suicide in the Case Diary. 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.
=== Writ Petition to Kerala High Court ===
The Action Council filed another Writ petition in the Kerala High Court asking the court to remove V. Thyagarajan from Cochin Unit of the CBI as well as from the investigation. Further on 3 June 1994 all the Members of Parliament 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. As a result, M.L. Sharma, the Joint Director of the CBI, was given charge of the investigation into Abhaya's death.
== Cause of death==
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. He later made a statement before the Magistrate on 1 January 2009. The crime branch did not allow him to visit the crime scene to form a definite opinion as to the cause of death. The explanation of the crime branch is that the case had been handed over to the state forensic chief Dr. Umadathan. 
Dr. Radhakrishnan noted six homicidal injuries on the body of the deceased.
Sr. Abhaya had the following ante-mortem injuries as per the post-mortem certificate issued by Dr. Radhakrishnan:
1. Lacerated wound 1.8x0.5x0.2 cm., oblique, on the right side of the back of head, the upper end being 3 cm above end 3 cm behind the top of ear.
2. Lacerated wound 1.5x0.5x0.3 cm, oblique, on the head 2.5 cm behind injury No.1.
3. 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.
4. Abrasion 1.5x1 cm., 2 cm below injury No.3.
5. Multiple graze abrasions over an area 12 x 6 cm on the outer aspect of right buttock, the upper boarder being 4 cm below iliac crest. The direction of the grazes were upwards and inwards.
6. On dissection the scale tissues over an area 2 x2 cm on middle of the top of head were found contused. The scalp tissues over an area 7 x 5 cm around injuries Nos.1 and 2 were also found contused. 
The skull was intact. Brain showed localised sub-arachnoid haemorrhage underneath these contused regions. No sign of increased intra-cranial tension." 
=== CBI's dummy test ===
On the 7 April 1995, using a full-sized dummy of Sister Abhaya, the CBI made some experimental tests in the well where her corpse was found. Based on the post mortem report, On 17 April 1995 Dr. S.K. 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. Subsequently, the CBI declared that the killers would soon be arrested.
=== Protest continuing ===
After the dummy test no arrests were made. The investigation itself was limping without a clear aim before them. Hence the Action Council staged a protest in front of the CBI office at Cochin on 27 November 1995 against the callousness of the CBI and its lack of orientation. Later on 18 March 1996 another big rally was organised under the leadership of former chief minister of the state, E.K. Nayanar, in front of the state secretariat, at Thiruvananthapuram, the state capital. Again on 1 July 1996 the Action Council filed a petition in the High Court challenging the inaction of the CBI. The High Court passed an order in the petition on 20 August 1996 directing the CBI to complete its investigation in three months from the date of the order. In the meantime, the CBI declared an award of 300,000 rupees to whoever gives dependable evidence in the case of Abhaya.
On 12 October 1996 all the Members of Parliament] from Kerala together visited the Prime Minister and jointly pleaded with him to expedite the CBI investigation into the death of Abhaya. However, on 6 December 1996 the CBI filed a petition in the Chief Judicial Magistrate's court, Ernakulam, seeking permission of the court to wind up its investigation in the matter for want of evidence. The court refused permission and directed the CBI to continue the investigation.
=== Court criticizing CBI ===
The Chief Judicial Magistrate (CJM) directed the CBI in its order dated 20 March 1997 to re-investigate the case. The court in its order strongly criticized the CBI for its loyalty and complicity to certain vested interests to defeat the ends of justice and the court observed that the CBI had not made party some very significant persons who otherwise emerged in the facts of the case quite evidently. The court also asserted its belief that the case could have easily been established had there been an honest and proper investigation. Further the court after seeing the video cassette of an Asianet interview, mentioned K.T. Michael by name for "influencing" the course of the investigation. This remark was later expunged by the High Court, after considering the reasons for the statements made during the interview. The CJM court observed that certain "invisible hands" were still trying to scuttle the Sister Abhaya murder case observing that these forces were trying to influence the investigating agencies and the government officials.
=== High Court’s new intervention ===
The Action Council, again on 30 May 1997 filed a Public Interest Litigation in the High Court of Kerala against the non-compliance of the CJM's directive for re-investigation. The High Court in its order directed the CBI to report back to the court the progress it had made in the investigation in ten days from the date of the order.
Having had enough of the failure and lack of interest on the part of the CBI, the High Court directed suo moto the Director of the CBI to appoint a special team from New Delhi to investigate the matter. Thus P.D. Meena, the Superintendent of the CBI from New Delhi and his team undertook a month-long investigation and reported to the High Court. The CBI was convinced that the death of Abhaya was in fact murder. However, the CBI report said that due to lack of evidence it was not possible to go further into the matter. The High Court again on 28 September 1998 directed the CBI to file its final report of the re-investigation on or before 12 October 1998.
The magistrate court later affirmed that there was clear evidence to show that some officers who took part in the investigation conducted by the local police and Crime Branch wanted to refer this case as a case of suicide. The remarks were later expunged by the High Court.
== CJM directs CBI to use modern methods of investigation 2000==
The then Chief Judicial Magistrate (CJM), Ernakulam, Mr Antony T Moraes in his order dated 23 June 2000, directed the CBI to conduct a detailed investigation regarding the destruction of the property involved in this case and the reason thereof. He also directed the CBI to question Fr Thomas Thazhampally who has stated that Abhaya was murdered and hinted about the involvement of a priest who was roaming around on a scooter. He had further directed the CBI to use modern scientific means of identifying the actual accused of the crime using Dr Farwell's Brain fingerprinting of the suspects.
The case was in cold storage for nearly seven years and was considered closed.
== Developments since 2007 ==
A report by B. Sreejan, senior reporter with the Thiruvananthapuram bureau of The New Indian Express (12 April 2007), stated that the original chemical examination report of the vagina swab and vaginal smear of Abhaya has been found to have been tampered with. The manuscript of the workbook report from the Chemical Examination Laboratory shows over-writing in four places. Using a whitener and a different ink, the word ‘‘not’’ has been added to the word ‘‘detected,’. The lab explained that it was quite normal to make corrections in the manuscript. Even Varghese P Thomas, the first investigating officer, said the post mortem and lab reports had ruled out rape, leaving no scope for suspicions on the veracity of the report. 
===Narco analysis tests===
As part of its investigation in August 2007, the CBI conducted Narco Analysis tests on Fr.Thomas Kottoor , Fr. Jose Poothrikkayil, Sr. Sephy and some others whom they believed had knowledge about the case. Narco Analysis test report and CD were sent to the Chief Judicial Magistrate Court and to the High Court.
There were allegations that the CDs relating to the narco analysis tests were manipulated. Justice Ramkumar of the Kerala High Court sent questionnaires to Dr. Malini, Assistant Director of the Bangalore centre where the narco analysis was conducted. The lab denied any manipulation. 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. 
Dr. Malathi has since been dismissed from service on the charge of forging her birth certificates.
CDAC Trivandrum, ordered by the Ernakulam CJM court to verify the Narco CDS submits that they are not equipped for the tests. CDs given to CDIT for tests. CDIT submits the finding that the CDs have been doctored more than 30 times. Court orders CBi to find out the original CDs. within 10 days. CBI questions the forensic lab officials including Dr. Malini. CBi makes a volte face and submits that the CDs were not edited. CDIT challenges the submission by CBI. Abhaya's father files contempt of court petition against CBI for not producing original CDs.
=== 2008 ===
On January 11, 2008, the Kerala High Court directed the CBI to produce the result of the Narco-analysis test conducted on the suspects in the case in a sealed cover before the court within two weeks. The court further directed that no third person had any right of disclosure of the content of the results till the appropriate stage, other than the High Court. In this regard, the CBI submitted it before the court on January 21, 2008. The results were submitted in a sealed cover as directed by the court. 
=== Allegations regarding community leaders trying to sabotage the case===
Since the incident happens to involve religion and sensitive elements it always created controversy. There were wide speculations that an influential Christian political leader from Central Kerala tried to sabotage the case by influencing the then Congress government in the centre. Other allegations include the Catholic Church Council trying to influence the outcome of the investigations. Others also allege 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.
== The arrests ==
CBI arrested two Knanaya Catholic priests, Fr. Thomas Kottoor, Fr . Jose Puthrukayil and a Knanaya nun Sr. Sephy on 19 November 2008.Two priests and nun held-The Hindu
On November 22, 2008 Archbishop Kuriakose Kunnacherry, former head of the Archdiocese of Kottayam, was summoned for questioning.Church head to be questioned-The Hindu The CBI, questioned Kottayam Archbishop Mathew Moolekkatt at its office in Kochi on November 24, 2008.Sify News
On November 25, 2008 V.V. Augustine, the Assistant Sub Inspector who prepared the First Information Report during initial investigation of case was found dead. Police said he committed suicide by cutting the artery on his wrist and also taking poison. A suicide note cited mental torture by CBI. The CBI had alleged that Augustine had destroyed evidence and connived to close the case as suicide. But the case diary revealed that it was in fact Augustine who pointed to the possibility of homicide. He had recorded that Abhaya would have seen something objectionable in the dining room and could have been silenced.Former Police Officer Dead-The Hindu
Augustine's suicide note indicated the level of harassment by the CBI even 16 years after the incident. He wrote that CBI is the sole cause of his death. In his personal diary, Augustine wrote about how he was pressured by CBI to say that senior police officers tried to influence him. In short, the CBI had threatened Augustine to support their theory. Augustine did not comply and committed suicide.
On Dec 02, 2008 and on December 29, 2008, Central Bureau of Investigation (CBI), made a statement before P. D. Soman, Chief Judicial Magistrate, Ernakulam. According to the CBI, their brain-mapping and narco analysis investigations revealed that Sister Abhaya woke up on March 27, 1992, early in the morning, descended the staircase and went to the hostel kitchen to get a drink of water from the refrigerator. Sr. Sefi hit Abhaya with an axe ('kodali') thrice on the back of the head, near the right ear and on the head. She then collapsed. Thinking that Abhaya was dead, Fr. Thomas Kottoor, and Fr. Jose Poothrikkayil, assisted by Sr. Sephy, lifted Sr Abhaya's body, took it out of the kitchen and dumped in a well behind the building.Sr Abhaya hit with an axe. The HinduAll accused admits to crime:CBI The Hindu
On 1 January 2009, in a controversial judgment, Justice Hema of the Kerala High Court, granted conditional bail to the three accused, passing strictures against the CBI investigation. She stated that the arguments of the CBI counsel were not based on the facts as recorded in the case diary.
=== Motives ===
The CBI informed the Kerala High Court in late November 2008 and early December 2008 that Sister Abhaya had accidentally intruded upon Sr. Sephi and the other two accused priests in a "compromising position". Sr Sephi panicked and, on the spur of the moment, Sephie hit her with an axe meant for chopping firewood. The three accused together dumped Abhaya's body into the well.
CBI also informed the High Court about the remarkable degree of care the accused took to hide the crime. This allegedly included the bizarre claim of a hymen-restoration (Hymenoplasty or Hymenorrhaphy) procedure on Sr. Sephy which was discovered through gynecological tests conducted on her in late 2008. This was strongly refuted by the accused. The counsel for the accused dared CBI to prove that such an operation has ever been conducted in India. Further, the building where the crime was allegedly committed was extensively remodeled. The accused used their personal and church influence with the political system and bureaucracy to systematically sabotage the investigations in the case.
=== Protests by the Knanaya Community and Catholic Church ===
The Catholic Church and Knanaya community in Kerala protested against the arrests of the priests and nun. According to them, all the investigations were prejudiced and targeted at the priests and nuns. There were reasons to suspect the involvement of others including the four boys and two girls who were rounded up by the police in Alappuzha, 13 days before Abhaya's murder, leading to expulsion of the two girls from the hostel. There were threatening calls to the convent hostel until Abhaya's death. The two boys attempted suicide immediately after Abhaya's death and one of the boys Biju Panicker of Ranni, is still not traceable by the family. The Church also protested against the trial by the media, prejudging that the priests and the nuns were the culprits in this case. The church and convent stated that they had always cooperated with the investigators and did not try to influence anyone. It was the Mother Superior of the Sisters who sought a CBI investigation into the case, in the initial stages. These facts were highlighted by Justice Hema of Kerala High Court in her judgment while granting bail to the three arrested priests and nun.
;Bail Petitions (7508/08, 7551/08 and 7313/08) before Justice Hema
Arguments by CBI
1. Disturbance in kitchen.
2. Narco reports.
3. Local police tried to write it off as suicide.
4. ASI Augustine suppressed facts.
5. Church influenced police to suppress the murder.
6. Opinion of expert doctors outside Kerala.
7. Adakka Raju, a thief present on the terrace saw two persons climbing the stairs.
8. Sanju P Mathew, neighbour, saw scooter of Fr. Kottoor in the convent poch the previous night.
9. Kottor informed one Venugopalan Nair that he was guilty.
10. Several priests and nuns stated about the illicit relationd between the priests and nuns in the convent.
Arguments by the accused
1. Innocent.
2. Sr. Abhaya committed suicide.
3. Not a single drop of blood anywhere in the crime scene.
4. The scenario as stated by the CBI not possible at the crime scene.
5. The wounds not possible with the alleged murder weapon.
6. Post mortem report says it is suicide.
7. Narco analysis tests proved the innocence and not guilt of the accused.
8. High Court in case WPC 55590/07 said Narco CDs were tampered.
9. CBI was forced to arrest the accused to save its face and to avoid criticism by High Court.
10. CBI was encouraged by the comments of the court in the earlier case to make false arrests.
11. Statements by Adakka Raju and sanju P Thomas obtaiend by CBI under duress and that too after 16 years.
12. Alleged statements by priests and nuns are just heresay.
== Bail granted for the accused ==
Kerala High Court Judge Justice K. Hema granted bail to the three accused in her judgment delivered on 1 January 2009. She had earlier observed that the arguments of the CBI counsel were contrary to the facts recorded in the case diary. and seemed to be based on the stories appearing in the media.
The counsel responded that the arguments had been accepted by the earlier courts. The observation made by the High Court about the CBI investigation was “ All together on a close perusal of the case diary I find that there is only a chase for the shadow rather the object in this case. This chase is only a futile exercise. Investigation means to carefully examine the facts of a situation, an event, a crime, etc., to find out the truth about it or how it happened. It is not to fix the target first, without any evidence and then make a hunt for evidence.”(Page 43, Para 89. Bail Judgement by Hon’le Justice K. Hema dated 01.01.’09)
The judgement also severely criticises the media and the public which pronounced the verdict beforehand knowing very little about the actual facts of the case, 24 volumes of case diary, the medical reports and the statements from the doctors. The judgement also makes mention of the accusations propagated by the media, public and the CBI against officers of the local police, crime branch without any incriminating evidence.
The judgment contains several adverse observations on the evidence and CBI investigation. She refuted the argument that ASI Augustine tried to suppress facts. The case diary reveals that it was Augustine, who was in charge of the case for only two days, who recorded the possibility of murder and mentioned the possible scenario now stated by the CBI. The judge also observed that nowhere in the case diary, there is any mention that the church had tried to influence the investigation. Contrary to the public perception that the CBI enquiry was ordered on the request of the Action Council, it was based on the request by the nuns of the congregation. The judge also made observations on the reliability of the narco analysis CDs and ordered production of the original CDs. A complete version of the judgement is available to the public in Sr. Sephy Pius X Convent vs. Union of Inida..
Justice Basant had earlier observed that he alone had the right to issue orders on the case which was publicly challenged by Justice Hema who said all judges had equal rights. The controversy generated by the open disagreements and comments forced Basanth, to recuse from the supervision of the case. The supervsion was entrusted to a Division Bench of the Kerala High Court. On 12 March 2009 High Court closed all the proceedings before it and entrusted CJM court Ernakulam to continue the proceedings before it.
==Judgment by Justice Hema==
Justice Hema's decision to grant bail to three accused in the Sister Abaya murder case seemed just and by the letter of the law. The media however disliked the verdict since it put an end to their tabloid fodder. The CBI, according to Justice Hema, was building their case around media suppositions and gossip. Earlier, the CBI had pleaded with the Chief Justice that the bail application should be moved out of Justice Hema's court as she was "prejudiced towards the case". The request was rejected by a division bench. The order of Hema that a senior officer should supervise the investigation was challenged by the CBI before Justice Basanth who was in charge of monitoring the case. He ordered that he alone can monitor the case. This was disputed by Hema while hearing another case. She said all High Court judges have equal powers and her order can be challenged only before a division bench. She said that Justice Basanth and others had not thoroughly examined the case diary and this was evident by Justice Basanth's resignation from the case later. The case has since been placed before a division bench of the High Court.http://www.indianexpress.com/news/hc-grants-bail-to-abhaya-case-accused-raps-cbi/405532Kerala Kaumudi reported under the editorial title "The comfort of blind-folded eves of the Goddess of Justice" that Judge Hema was being influenced by a retired judge of the Supreme Court, a Christian, under whom she had practised as a junior. to help the accused in Abhaya case. The reference was to Justice K.T. Thomas and was not a fact. Justice Thomas who used to practise at Kottayam had long before became a judge, when Hema started practise at Calicut under K Bhaskaran Nair. Justice Thomas had earlier written a newspaper article, questioning the accuracy and admissibility of narco tests as eveidence. Later, based on the decision of the full bench of the High court, a Division Bench of the High Court initiated criminal contempt of court proceedings against the news paper on the basis of the editorial. On 23 March 2009 Kerala Kaumudi submitted its unconditional apology, based on whcich the High Court closed the contempt of court case.http://www.expressbuzz.com/edition/story.aspx?Title=Criminal+contempt+case+against+Kerala+Kaumudi&artid=h|geQmDztLg=&SectionID=1ZkF/jmWuSA=&MainSectionID=fyV9T2jIa4A=&SectionName=X7s7i|xOZ5Y=&SEO=Kerala+High+Court;+M+S+Ravi,+the+printer+and+publi
==Limitations of brain mapping as a crime investigation tool and evidence==
M Raghava, columnist, reported in 'The Hindu' on September 6, 2008, the results of the study of an expert committee headed by NIMHANS, Bangalore, that recommended that brain mapping as an investigative tool and evidence, must be stopped. It says:
"An expert committee studying the efficacy of brain mapping criminal suspects has concluded that it is unscientific and should be discontinued as an investigative tool and as evidence in courts... In its findings, the committee said there were several factors that came in the way of a dependable and conclusive outcome. For instance, body temperature, heart rate and menstrual cycle, induced factors such as exercise, fatigue, drugs and alcohol and constitutional factors such as age, intelligence, gender and personality of the individual all played a role which needed to be taken into account, something the existing method does not. For use as a forensic tool, a procedure needed to have established error rates. But brain mapping as done in the Forensic Science Laboratories (FSL) in Bangalore and a variation called brain electrical oscillation signature (BEOS) profiling in Gandhinagar, Gujarat, had not worked on this factor, the committee said.
Besides Mr. Nagaraj, the committee comprised Narayanan Srinivasan, Senior Faculty, Center for Behavioural and Cognitive Sciences, University of Allahabad; Narayanan Dutt, Professor, Department of ECE, Indian Institute of Science, Bangalore; N. Pradhan, Professor and head of the Department of Psychopharmacology, NIMHANS; Venkatasubramanian, Assistant Professor of Psychiatry, NIMHANS; and M.S. Rao, Director and Chief Forensic Scientist, Directorate of Forensic Science, New Delhi.
In a typical criminal investigation, suspects first undergo a lie detection test followed by brain mapping and narco-analysis.
The team began its study in May 2007 at the request of the Directorate of Forensic Sciences of the Ministry of Home Affairs.
The relevant portions of the judgement of Justice Hema are given below: 
"51. Brain finger printing report negatives accuseds' involvement: Learned Standing Counsel for CBI placed strong reliance upon the Brain Fingerprinting Report to argue that the involvement of the accused is proved by such report. A report dated 12. 06. 2003 by Dr. Mukundan on Brain Fingerprinting investigation reveals that several individuals were subjected to Brain Fingerprinting Investigation at the National Institute of Mental Health and Nuero Sciences, Bangalore, in relation with the death of Sr. Abhaya on 27.3.1992. They include the accused and various other suspects also.
52. The report shows that the second and third accused were tested with probes suggesting direct involvement in the death of Sr. Abhaya and it is reported that they "have not shown any brain activation pattern supporting experimental knowledge of such an act". Learned counsel for the accused also pointed out that this fact was taken note of by the CBI itself and it is stated in the final report dated 25.8.2005 submitted by Sri.R.R. Sahay, Additional Superintendent of Police. The relevant portion from the said report is as follows: "regarding the three suspects Sanju P. Mathew, Sr. Sephy and Fr. Poothrikkayil for probe of direct involvement in the death of Sr. Abhaya NIMHANS has reported that they did not show any brain activation pattern supporting experimental knowledge of such an act."
53. That means, the Brain Fingerprinting investigation report negatives the experience of second and third accused in the alleged murder of Sr. Abhaya and their involvement in the murder and this fact is accepted also by CBI. It is not understood why arguments are still, advanced contrary to the scientific reports and the reports submitted by CBI itself that those reports prove involvement of accused in murder. (The polygraph tests also gave negative reports regarding their involvement in alleged murder)." ''
== CBI filed charge sheet against the accused ==
On 17 July 2009 CBI Filed charge sheet. The CBI website summarises the case as follows:
" The CBI, Kochi Branch, today filed chargesheet in the Court of Chief Judicial Magistrate, Ernakulam, against the 3 accused, viz.. two Fathers and one Sister in Sister Abhaya Murder case. The chargesheet was filed under Sections 302, 201 and 449 r/w 34 IPC. 
Sister Abhaya @ Beena Thomas, a Christian nun, was a student of BCM College, Kottayam, for Pre-degree and was residing at St. Pius X Convent Hostel, Kottayam, Kerala. Female students and nuns were the occupants of the Convent Hostel. On 27.3.1992 in the morning, Sister Abhaya's dead body was found in the well of the Hostel inside the compound. The case was initially investigated by local Police in F.I.R. No.187/92, dated 27.3.92 registered under Sec.174 Cr.PC (Unnatural death). The Crime Branch, CID took over the investigation and filed a Closure Report on 30.1.93 on the ground that Sister Abhaya had committed suicide. The Closure Report was not accepted by the Chief Judicial Magistrate, Ernakulam. Subsequently, on the request of Government of Kerala, the case was registered by the CBI. The investigation conducted showed that Sister Abhaya had been murdered. 
The CBI continued its investigation and resorted to scientific methods including Polygraph Test, Brain Mapping Test, Brain Finger Printing Test and Narco Analysis, which pointed the needle of suspicion to the 3 accused persons. Sustained investigation, focussing on the movements of the accused and their conduct before and after the crime, resulted in unearthing vital evidence. Two male accused were arrested on 18.11.08 and another female accused was arrested on 19.11.08. 
The investigation disclosed that the chappals, veil etc., of the victim had been found scattered in the Kitchen/Wash area on the Cellar Floor of the Convent. The accused Sister was the sole occupant of the Cellar Floor on the night when the crime took place. The well, where the dead body of Sister Abhaya had been found, was at a hearing distance from the window of the room occupied by the 3rd accused in the Cellar Floor. The investigation also disclosed that two male accused were in the habit of making nocturnal visits to the Convent Hostel and were known to be close to another female accused. They were present with the 3rd accused on the fateful night. In the early morning of 27.3.92, Sister Abhaya went down from her 1st floor room to the kitchen for taking water from the fridge when she saw the accused in suspicious circumstances. The two male accused were her Teachers in the BCM College, Kottayam. Fearing that Sister Abhaya might speak to others about what she saw, the three accused entertained a common intention to kill her. She was hit on the head with a blunt weapon as a result of which she became unconscious and fell down. Not knowing as to how to dispose of the body of Sr. Abhaya, the accused tried to give it a colour of suicide by throwing the body from the fifth floor of the convent, but finding it difficult to do that, she was thrown in the well where she died due to drowning. 
The investigation disclosed that attempts had been made to hush up the case to make it appear as suicide. Shri V.V. Augustine, ASI, who had visited the spot, failed to take the suspected weapon of offence into his custody, tampered with the vital evidence, did not make a proper Inquest and forged the signatures of the witnesses on the Inquest Report. During the course of the investigation of the case, Shri V.V. Augustine was found dead on 25.11.08 in an isolated place near his house and as such he is cited as accused not sent up for trial. 
The chargesheet cites 133 witnesses, 67 documents and 7 Material Objects. 
The public is reminded that the above findings of the CBI are not the final proof of guilt of the accused. Under the Indian law the accused are presumed to be innocent till their guilt is finally established after a fair trial."
==References==
Category:Knanaya Community