KOCHI, India — When Bishop Franco Mulakkal agreed to personally celebrate the First Communion for Darly’s son, a rare honor in their Catholic Church in India, the family was overcome with pride.

During the ceremony, Darly looked over at her sister, a nun who worked with the bishop, to see her eyes spilling over with tears — tears of joy, she figured. But only later would she learn of her sister’s allegation that the night before, the bishop had summoned the nun to his quarters and raped her. The family says that was the first assault in a two-year ordeal in which the prelate raped her 13 times. The bishop, who has maintained his innocence, will be charged and face trial by a special prosecutor on accusations of rape and intimidation, the police investigating the case said. But the church acknowledged the nun’s accusations only after five of her fellow nuns mutinied and publicly rallied to her side to draw attention to her yearlong quest for justice, despite what they described as heavy pressure to remain silent.