At the Convent of the Order of the Servants of Mary in Calcutta, Sister Clodagh is instructed by her order to oversee the establishment of a new school and hospital at Mopu in the Himalayas. The local General has offered the use of a deserted palace, which was briefly home to a monastery, but originally built as a home for the dead General's concubines.

Sister Clodagh sets off with a team of four, picked for her by the Mother Superior: Sister Briony, for her strength, Sister 'Honey' Blanche, for her popularity, Sister Philippa, for the garden, and Sister Ruth, who has suffered from poor health and whose commitment to the Order is uncertain. Arriving at the palace, renamed the House of St Faith, the nuns are greeted by the old caretaker Ayah and a child, Joseph Anthony. They are still unpacking when they find the school and dispensary full of villagers who, they learn have been paid by the General to attend. Later Sister Clodagh is visited by the General's agent, the arrogant and cynical Mr Dean. Dean is dismissive of the Order's chances at the palace, and predicts they will leave before the rains come.

The climate at Mopu is inhospitable, and the nuns find the going tough. Dean tells Sister Clodagh to be wary of treating serious medical cases, warning that the villagers will turn against them if there is a death. When an excited Sister Ruth bursts in to tell of her success in treating a patient with a burst artery, Sister Clodagh chastises her for failing to summon the medically trained Sister Briony, but Dean, sensing that Sister Ruth is aggrieved, commends her.

Later, Dean returns to the convent with a young village girl, Kanchi. Dean explains that Kanchi has been following him around and causing a nuisance for her family, who are unable to marry her off. Reluctantly, Sister Clodagh agrees to take her in. When the young General, the old General's nephew, presents himself to Sister Clodagh and asks to be educated in the school, Clodagh feels duty bound to accept him, but is uneasy about Kanchi being in his presence.

Christmas arrives, and Sister Clodagh becomes nostalgic about a lost love. Dean turns up at the Christmas service drunk, and Sister Clodagh demands he not visit again. Later, conscious that Sister Ruth has been watching Dean, she attempts to talk to her about her health, and about Dean. Sister Ruth is defiant, accusing Sister Clodagh of being attracted to Dean herself.

Spring comes. When a gold chain goes missing, Kanchi is blamed and beaten by Aya, until the young General intervenes. As the flowers bloom, Sister Clodagh discovers that Sister Philippa has planted the garden entirely with flowers instead of vegetables. Confronted, Sister Philippa asks to leave Mopu.

When a sick baby is brought to the dispensary, Sister Briony, knowing she cannot help him, refuses to treat him. However, Sister Blanche secretly offers the mother medicine. When the baby dies, the nuns find the school and dispensary abandoned by the villagers. The young General and Kanchi have also disappeared.

Isolated, and warned by Aya not to visit the village, the nuns have no option but to summon Mr. Dean. Sister Clodagh, unaware that she is being watched by Sister Ruth, confides in Dean her fears about Mopu and her own tormented memories. Dean advises her to abandon the nunnery. That night, Sister Clodagh, unable to sleep sees a light in Sister Ruth's room. When Sister Ruth opens the door, she wears a striking red evening dress in place of her nun's habit. She informs Sister Clodagh defiantly that she has left the Order and is leaving the nunnery. Sister Clodagh begs her to wait until morning, and settles down to wait with her. But she falls asleep, and wakes to see Sister Ruth rushing out of the room. Sister Clodagh calls the other Sisters, but they are unable to catch her.

Sister Ruth makes her way down the mountain to the empty house of Mr. Dean. When Dean returns, she professes her love for him, but he rejects her. Seeing that she is sick, he offers to return with her to the nunnery, but she refuses and leaves alone. Sister Ruth makes her way back to the nunnery, where she watches Sister Clodagh in the chapel. As Sister Clodagh goes out to ring the morning bell, Sister Ruth rushes from the chapel and attacks her. There is a struggle and Sister Ruth falls to her death.

The surviving nuns prepare to abandon the nunnery. As they are making their way, they are met on the path by Mr. Dean. He and Sister Clodagh say their goodbyes, and as Dean moves away, the rains begin to fall.