Crime File movie is based on the murder of a Christian nun Sister Abhaya of Kottayam. Sister Amala (Sangeetha) who is an outspoken, often blasphemous, legal expert who takes on anything and anybody evil. Amala has a lot of enemies, even inside the church set-up. Even the bishop of the diocese (Jagannatha Varma), his lesser clergy, the local political don Mammachan of Kairali Congress (Rajan P Dev) and the assembly member from the place, Monayi (Vijayakumar) hold her enemy number one.
Amala obviously peeps into a lot of intriguing sanctum sanctorum and has a collection of evidence against certain highly influential person(s). She prepares to approach the court with unbeatable proof against certain top gun on the murder of an erstwhile ruffian-on-rent (Ganesh). Soon she gets dropped to death, to be found by another nun, in the 40-foot deep well that has three-foot deep water. Who killed Sister Amala?