After recovering from tetrodotoxin poisoning inflicted by the SMERSH agent Rosa Klebb (see From Russia, with Love) MI6 agent James Bond is sent by his superior, M, on a "rest cure" to Jamaica. Whilst there his task is a simple assignment to investigate the disappearance of Commander John Strangways, the head of MI6 Station J in Kingston, Jamaica, and his secretary.
Bond is briefed that Strangways had been investigating the activities of Dr. Julius No, a reclusive Chinese-German who lives on Crab Key and runs a guano mine; the island is said to be the home of a vicious dragon, and has a colony of Roseate Spoonbills at one end. The Spoonbills are protected by the National Audubon Society, two of whose representatives had died when their plane crashed on Dr. No's airstrip. On his arrival in Jamaica, Bond soon realises that he is being watched, as his hotel room is searched, a basket of poisoned fruit is delivered to his hotel room (supposedly a gift from the colonial governor) and a deadly centipede is placed in his bed while he is sleeping.
With the help of his old friend Quarrel, Bond visits Crab Key to establish if there is a connection between Dr. No and Strangways' disappearance. There he and Quarrel meet Honeychile Rider, who visits the island to collect valuable shells. Bond and Honey are captured by No's men after Quarrel is burned to death by the doctor's "dragon" – a flamethrowing armoured swamp buggy to keep away trespassers.
Bond discovers that Dr. No is also working with the Russians and has built an elaborate underground facility from which he can sabotage American missile tests at nearby Cape Canaveral. No had previously been a member of a Chinese Tong, but after he stole a large amount of money from their treasury, he was captured by the organisation, whose leaders had his hands cut off as a sign of punishment for theft, and then ordered him shot. The Tong thought they shot him through the heart. However, because No's heart was on the right side of his body (dextrocardia), the bullet missed his heart and he survived. Interested in the ability of the human body to withstand and survive pain, No forces Bond to navigate his way through an obstacle course constructed in the facility's ventilation system. He is kept under regular observation, suffering electric shocks, burns and an encounter with large poisonous spiders along the way. The ordeal ends in a fight against a captive giant squid, which Bond defeats by using improvised and stolen objects made into weapons. After his escape, he encounters Honey from her ordeal where she had been pegged out to be eaten by crabs; the crabs ignored her and she had managed to make good her own escape.
Bond kills Dr. No by taking over the guano-loading machine at the docks and diverting the guano flow from it to bury the villain alive. Bond and Honey then escape from No's complex in the dragon buggy.