Judge J Nazar dismissed the petitions of Father Dr Thomas Kottoor, and Sister Sephy, the first and third accused respectively, seeking their discharge.
He observed that there was sufficient ground for presuming that the two had committed offences punishable under Indian Penal Code sections 302 (murder) and 201 (destroying evidences) read with section 34 (Acts done by several persons in furtherance of common intention).
However, the Judge allowed the discharge petition of second accused Father Jose Poothrikkayil, holding that the prosecution had failed to bring out sufficient materials to proceed against him.
Initially, the case was investigated by the local police and state crime branch which concluded that Abhaya had committed suicide.
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However, the case was taken over by CBI on March 29, 1993 following a legal battle by human rights activist Jomon Puthenpurackal.
The central probe agency in 2008 arrested Kottoor, Poothrikkayil and Sephy on the charge of murder.
According to the prosecution, Kottoor and Poothrikkayil were allegedly having an illicit relationship with Sephy, also an inmate of the convent.
The accused were arrested in 2008 and released on bail by the Kerala High Court a year later.