"Rain" opens on a steamer ship bound for American Samoa. Dr. Macphail, the story's protagonist and point-of-view character, stands at the railing. He is smoking. Soon he notices his wife talking to the Davidsons, a Christian missionary couple who have been stationed in a district of islands in Samoa. The two couples befriended each other on the cruise based on their shared disapproval for other passengers, who spend their days and nights gambling and drinking.
The next morning, Dr. Macphail stands on the deck talking to Mrs. Davidson. As the ship is approaching the port of Pago Pago, where they will board a schooner bound for the capital Apia, Mrs. Davidson remarks that she is glad that she and her husband are not stationed in this area. She speaks disparagingly of the natives in their district, and their marriage customs, to which the Davidsons responded by forbidding the natives from dancing, as they thought the traditional Samoan dancing led to immorality. As the ship approaches the harbor, Dr. Macphail is amazed by the native traders' medical problems, such as elephantiasis, and Mrs. Davidson can’t refrain from pointing out the indecency of their clothing. She also proudly adds that at their islands they have managed to eradicate the native custom of wearing loincloths almost completely.
On land, Mr. Davidson joins the party bearing bad news. One of the members of the crew of the schooner that is supposed to transport the travelers has fallen ill with measles. Consequently, the schooner is forbidden from entering the harbor until it is certain that no other passengers are ill. It’s raining and there is no hotel on the island, so the two couples have no choice but to rent poorly furnished rooms in a private house owned by Mr. Horn, a half-white, half-native trader.
The travelers cannot leave the island, so they spend their time together. Meanwhile, Mr. Davidson talks about the hard work that awaited him when he first came to the Pacific. He says his greatest achievement consisted of installing the sense of sin in the natives, who had previously thought their customs to be natural human behavior.
One evening when the Davidsons and the Macphails are having dinner, they hear a gramophone and the clinking of glasses from the room downstairs, where fellow traveler Miss Thompson resides. After a while, Mr. Davidson exclaims that she boarded the steamer at Honolulu and so must be a prostitute from Iwelei, the red-light district. He realizes she must be carrying on her trade here. Outraged, the missionary decides to take the matter into his own hands. He rushes downstairs and hurls the gramophone on the floor, but his intervention is of no use, as he is thrown out and the party continues.
The next day, during dinner, Mr. Davidson asks a Samoan girl to set up an appointment for him with Miss Thompson. He visits her after dinner and remains for an hour. He returns without having succeeded and declares that she is an evil woman, but he vows to pursue her "to the uttermost parts of the earth." Later, Dr. Macphail finds out that the missionary has asked the trader, Mr. Horn, to forbid Miss Thompson from having her customers in. During the night, the doctor and his wife hear Mr. Davidson pray aloud for Miss Thompson’s soul.
A couple of days later, when the two couples are dining, the door flings open on the dining room and Miss Thompson enters. She insults the missionary and inquires about what he has been saying to the governor about her, because apparently she was asked to leave on the next boat. She is being deported in five days on a boat to San Francisco.
The next day Miss Thompson pretends to be ill and calls Dr. Macphail to her room. She wants him to ask the missionary if he would let her stay for a fortnight so she can take a boat to Sydney and get a "straight" job there. Macphail assures her that Davidson will not allow that, but he promises to ask.
Macphail’s prediction turns out to be right, but he promises Miss Thompson to see the governor himself. The governor sees the doctor’s point, but he refuses to take back an order that he had already given, especially since Davidson threatened to complain about him back in Washington.
In the evening after dinner, Miss Thomson asks to see Mr. Davidson. She begs the missionary not to send her to San Francisco because she would have to go to prison for three years, but he is determined to make her accept her punishment. Miss Thompson has a breakdown and the doctor takes her back to her room. When he returns, the missionary asks everyone to pray with him for the young woman’s soul.
During the next couple of days, Miss Thomson turns into a wreck. She is apathetic and spends her days reading the Bible and praying with the missionary, who becomes ecstatic as he obsessively guides the young woman through repentance. The situation is so bad that she even starts to look forward to her punishment because it seems like an escape from the intolerable anguish of waiting. Meanwhile, the weather is horrid; it will not stop raining. On Monday, Miss Thomson receives a call telling her to be ready to leave the next day at 11.
In the middle of the night, Macphail is woken up by Mr. Horn. The trader leads him to the shore where a group of native people are waiting. When they open up the circle, the doctor sees the dead body of the missionary Davidson, with his throat cut from ear to ear, the razor in Davidson's right hand. He concludes it was a suicide.
Dr. Macphail asks his wife to break the news to Mrs. Davidson. The missionary’s wife wants to see her dead husband, so the Macphails accompany her to the mortuary. On their way back, they hear a gramophone playing loudly in the house. When they come in, they see Miss Thomson, a changed woman, wearing again her ostentatious clothing while she is chatting up a sailor. At the sight of Mrs. Davidson, Miss Thomson spits in her direction. The newly widowed woman runs upstairs, while the doctor runs into her room and removes the record from the gramophone. She asks him what the hell is he doing in her room. Dr. Macphail is confused. Miss Thomson exclaims that all men are the same, they are all pigs. The doctor gasps, understanding that she is referring to Davidson.
