The story begins in an observatory, where an astronomer notices that Mars, older than Earth, has experienced a sudden drop off in sea levels and temperature. Its inhabitants seek a way off of their planet in order to survive these changes, and they achieve this by firing themselves off of Mars in canisters. From Earth, one only sees sudden explosions on the surface of Mars, but this fascinates the scientific community.
One canister lands near the narrator's home. It opens and a Martian comes out. It is nearly the size of a bear and greyish with large eyes and tentacles. The Martians dislike Earth’s atmosphere and retreat back into the canister. A human delegation, including the astronomer, approaches while waving the white flag of peace. The Martians vaporize the humans with a Heat Ray before continuing to assemble their machinery.
The British military arrives, and the entire small town of Woking is stuck in a tense standoff. After receiving heavy fire from the military, the Heat Ray suddenly erupts. The narrator takes his wife to a neighboring town, hoping that she will be safer there. He returns to Woking to return a cart, but a new Martian weapon forces him to crash. The Martians have constructed Tripods—brutal, three-legged robots, manned by Martians. Each has a heat ray and a chemical weapon, known as Black Smoke. These Tripods quickly destroy most of the military and Woking, leaving wreckage in their wake. An artilleryman warns the narrator that another canister has landed nearby, which separates the narrator from his wife. The two try to escape Woking, and they hear that the military has taken down a Tripod by the Thames, a great victory.
The Martians are now retreating towards Woking. The narrator fashions a raft and tries to float down the Thames stopping at Walton. There, he meets a curate, with whom he teams up. The Martians break the line of defense around London and release the Black Smoke, causing a mass exodus from London. The novel's point of view then switches to the neighbors' brother, who is now a refugee from London. He flees to the Essex coast, a journey he completes with all the other refugees. The brother saves a family from being robbed, and the family then comes with him. They buy passage on a ship to America, but just as they are about to leave, Martians appear and almost destroy the ship. However, just in time, another ship called the HMS Thunder Child rams the Tripods, destroying itself but allowing the other ship filled with civilians to leave.
Soon after, the military crumbles and the Martians roam the British countryside free from any opposition. This is the end of Book 1.
Book 2 begins with the narrator and the curate searching houses for food. They see a new Martian machine, one that kidnaps any human it finds, throwing them into a container on its back. The narrator worries that the Martian’s purpose may be something far worse than mere destruction. A fifth cylinder lands, destroying the surrounding area and trapping the narrator and curate for two weeks. The curate begins to go mad, and the narrator is forced to knock him unconscious to keep him quiet. However, the Martians outside hear the noise and steal the curate's body. They take his blood to nourish themselves, and the narrator only barely escapes them. He later finds an invasive Martian plant growing all over the land and notices that it seems to only like places with very large quantities of water.
He re-encounters the artilleryman, who tells him of a plan to live underground and rebuild civilization, but his plan does not seem very well thought-out. The narrator starts to go mad in the streets of London and approaches a Martian machine with the intention of killing himself. However, he discovers that the Martians inside it are actually dead, having died from disease caused by the microbes in Earth’s atmosphere; the Martians had no immunity to these germs. The narrator has a nervous breakdown and is nursed back to health by a kind family. Eventually, he returns home and discovers that his wife is still alive.
The last part of the book reflects on the significance of the new Earth post-invasion, and on the new doubts and worries that fill the narrator's mind.
