The novel begins two years into Genly Ai’s Envoy mission to the planet Gethen. His task is to convince the Gethenian nations to join an interplanetary trade network known as the Ekumen. Eighty percent of the time, the people of Gethen are hermaphroditic neuters, meaning that Gethenians are neither male, nor female, and they only express sexual characteristics or desire during a period known as kemmer, which lasts for a few days every month. Because Ai is a Terran man, Gethenians see him as either an anomaly, an alien, or a sexual pervert.
Ai lives in Erhenrang, the capital of the nation of Karhide. The prime minister of Karhide, Therem Harth rem ir Estraven, has been helping Ai arrange a meeting with King Argaven to plead his case. Ai distrusts Estraven, but requires and accepts his help in order to further his mission. Unfortunately, the morning of Ai’s meeting, Estraven is announced to be a traitor and exiled. Ai’s proposal to the King—that Karhide join the Ekumen—is subsequently rejected.
After his proposal is rejected, Ai travels around Karhide, learning about its rural people, and one of its two religion, Handdara. He meets a group of Handdara Foretellers, who are able to see the future, and who inform him that within five years, Gethen will be a member of the Ekumen. After he meets with the Foretellers, Ai briefly returns to Erhenrang, but, feeling unsafe there, he decides to try his luck in another of Gethen’s nations. He crosses the border to Orgoreyn, where he is adopted by a faction of bureaucrats who initially seem more receptive to his mission than the governing body of Karhide.
In Orgoreyn, Ai is surprised to be reunited with Estraven, who has been in the country since his exile several months ago. Unbeknownst to Ai, Estraven, who had worked on Ai’s behalf in Karhide, has helped bring him to Orgoreyn, where he hopes the Envoy’s mission will be more successful.
Ai naively believes his mission is close to completion, but Estraven can see that political tides are turning, such that the Orgata Commensals who once supported Ai have turned against him. The Commensals either believe Ai to be a fraud, or believe him to be real and therefore a threat to their own power. They imprison him and send him north to a labor camp where he quickly falls ill. Estraven feels responsible for Ai’s arrival in Orgoreyn (and therefore his imprisonment), and hatches a plan to free him.
Estraven breaks Ai out of the labor camp, but only after Ai has spent almost a month getting sicker and sicker. The pair spends a few days recovering in a tent hidden in the mountains, before beginning the next stage of Estraven’s plan: because Ai is no longer welcome in Orgoreyn, they will return to Karhide. However, because of the risk of recapture, they must travel north across the Gorbin Ice, where the only threat will be the environment itself.
All this time Ai is still unable to fully trust Estraven, or understand why he has sacrificed so much to help him. Ai has yet to fully accept or understand Gethenian sexuality. Because he is unable to see Estraven as man or a woman, Ai feels him to be inherently deceptive. However, during the three months the pair spend traveling together across treacherous terrain, Ai finally begins to see Estraven as Estraven sees himself: as neither a man nor a woman, but a complex person who is at once both and neither. They become like brothers, and come to love each other.
More than eighty days after their journey first began, Ai and Estraven arrive in a village in Karhide. From there they travel to the town of Sassinoth, where Ai is able to send a radio signal to his spaceship. Ai hopes that the arrival of his shipmates will finally convince Argaven to join the Ekumen, and will help preserve his own life. Although end Ai’s mission is nearly complete, Estraven is still in danger, since he has returned to Karhide even though he has been exiled. After the government becomes aware of Estraven’s presence in Sassinoth, he flees to the border, where he is shot and killed by border guards.
Even as Ai mourns Estraven, he manages to negotiate with the King. He convinces the King to welcome his shipmates and join the Ekumen. The novel ends as Ai’s shipmates travel to the other Gethenian nations to convince them to join as well, thereby fulfilling their mission. Ai is happy that his grand objective has been achieved, but he feels obligated to complete one last task: he travels to Estraven’s home to deliver Estraven’s diaries to his estranged father and son.