There is talk of war in Europe; it is May, 1914, and Richard Hannay, a Scot, is starting afresh in London after time spent in Rhodesia (now Zimbabwe). He is gregarious and talks to strangers in passing, but one seems to attach himself more than the average casual acquaintance. Franklin P. Scudder is an American who is convinced that the world is about to erupt into war. He tells Hannay that he is actually dead, which of course intrigues Hannay, because it is not often one finds oneself talking to a dead man. Scudder elaborates and tells Hannay that he is a freelance spy and has faked his own death in order to be able to conduct his investigations more safely. He tells of a group of Germans chasing him, and Hannay offers to allow him to stay at his flat for a little while. Unfortunately this does not seem to throw the Germans off the scent; one evening, a man who lives in Hannay's building is murdered, and a couple of days after that, Hannay returns home to his flat to find that Hannay too has been murdered, stabbed in he heart.
This worries Hannay. What if the murderers come back for him or think he is somehow working with Scudder? He is also worried because he realizes he will be the prime suspect in the murder of a man staying in his flat. All things considered he decides it will be safer to head back to his native Scotland. He is convinced that the German spies are now watching him, and because of this he talks the milkman into letting him borrow his uniform so that he can sneak out of the building without being noticed. It works, and he manages to get to the train station to leave town. He is already thinking like a spy, and although he is going to a remote town called Galloway, he tells the ticket clerk that he is going to the small town of Newton Stewart. Once in Galloway, he finds a shepherd's cottage that is deserted and decides to stay there. However, he learns from reading the newspaper the next day that he is indeed a wanted man, and the police are looking for him in connection with the deaths of two men in his apartment building. He decides to keep moving; the police will probably believe him to have gone to the west coast, so the most logical thing for him to do is go to the east instead. Part way across the country by rail he jumps the train, and finds an inn to stay at for the night. When two men arrive at the inn looking for him, he steals their car whilst they are inside asking questions about him.
While he has been "on the run", Hannay has been reading Scudder's notebooks and he is struggling to solve most of the codes contained within it, but he does manage to solve a substitution cipher, which is making him question the stories that Scudder told him when they first met. The general suspicion that Britain is about to be invaded by Germany does seem to appear in the notebooks, though, and Hannay still believes that the men following him are German spies.
He hides in the countryside but it is getting more and more difficult to evade capture, especially when there are planes looking for him as well as the pursuers on foot. He meets a man mending the road, and the workman willingly trades clothes with him, and goes home, leaving Hannay working on the roadway in his place. His pursuers are fooled; they see him but do not notice him, and pass him by. Another change of clothes occurs when he randomly runs into someone he knows from London; they swap outfits and the Londoner drives him across the moorland, enabling him to pull off another miraculous escape. Hannay continues to stay a step ahead of his pursuers, always coming upon people who are willling to help him out However, his luck runs out when he engages the help of an elderly man who allows him to stay overnight at his cottage; the man is one of his enemies and locks Hannay into a store-room. Clearly the man did not think ahead; there is bomb-making equipment stored in the room and Hannay uses this to break out of the cottage, although he is injured during the escape.
The workman mending the road has been looking after his belongings since their encounter on the moors; he also allows Hannay to stay at his home to recuperate after escaping from the store-room. A few days later, feeling stronger again, Hannay takes a train back to England, but changes trains several times along the way in hopes of making it harder to trail him. Whilst in Scotland he had made acquaintance with a would-be politician named Sir Harry, and upon his arrival in Berkshire, in the south of England, seeks out Sir Harry's relative Sir Walter Bulivant, who works at the Foreign Office. Whilst the men are talking Sir Walter receives a telephone call and learns that the Greek Prime Minister Karolides has been assassinated during his official diplomatic visit to London; this is exactly what Scudder had predicted when he and Hannay first met. Sir Walter shares some military secrets with Hannay, and invites him to stay with him at his London home. As he leaves, he sees Sir Walter meeting with some important officials, one of whom, ostensibly a Chief of Staff with the Royal Navy, he recognizes as one of the men pursuing him. He tells Sir Walter that the man is not who he claims to be; he is a spy and is about to return to Europe with knowledge of British defense plans. He has deciphered the phrase "the thirty nine steps" several times in Scudder's notes, and now believes it might refer to the landing point on England's coast that the spy is planning on sailing home from.
Sir Walter, Hannay and the remaining team of strategists from the War Office brainstorm through the night and come to the conclusion that the location is a coastal town in Kent, where there is a path down from the cliff top that has thirty nine steps. They notice a yacht offshore and they disguise themselves as fishermen so that they have reason to approach. At least a couple of the yacht crew seem to be German. The people on the shore seem English, but they also match the descriptions that Scudder wrote in his notebook of the people who have been conspiring to invade Britain. Hannay is left alone on shore and decides to take the people on himself. Two of the men are captured but one runs away to the yacht, but he does not get far because British authorities seize it. The plot to steal British war strategy has been thwarted and as World War One breaks out, the secrets of the defense of the realm are kept. Hannay joins the army as soon as war is declared, and is immediately made a commissioned officer.
