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, which they get by firing themselves off of Mars in canisters. Earth only sees sudden explosions on the surface of Mars, which fascinates the scientific community. One canister lands near the narrator's home, and he discovers that it opens. A martian comes out, described as near the size of a bear, and greyish, with large eyes and tentacles. The Martians emerge, but dislike Earth’s atmosphere and retreat back into the canister. A human delegation, including the astronomer, approaches, waving a white flag. However, the Martians vaporize the humans with a Heat Ray, before beginning to assemble their machinery.
Human military quickly arrives, and the entire small town of Woking is stuck in a tense standoff. After heavy firing from the military, the Heat Ray suddenly erupts. The narrator takes his wife to a neighboring town, hoping that they will be safer there. He returns to Woking to return a cart, but a new Martian weapon forces him to crash his cart. 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 a trail of wreckage. A still-alive artilleryman warns the narrator that another canister has landed, which separated the narrator from his wife. The two try to escape Woking, and hear news that the military has taken down a Tripod by the Thames.
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, who he teams up with. The Martians break the line of defense around London and release the Black Smoke, causing a mass exodus from London. The point of view 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 they come with him. They buy passage on a ship to American, and as they were about to leave, Martians appear. They almost destroy the ship, but another ship, the HMS Thunder Child rams the Tripods, destroying itself, but allowing the other ship to leave.
Soon after, all resistance from any government stops, 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. It throws them into a container on its back. The narrator worries that the Martian’s purpose may not be destruction, but something worse. 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 out to keep him quiet. However, the Martians outside heard him, and steal his body. They take all of his blood to nourish themselves, and the narrator only barely escapes detection from the other Martians. He later escapes, and finds a Martian plant growing all over the land. 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. 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 are actually dead, all of them having been killed by the microbes in Earth’s atmosphere. The narrator has a nervous breakdown and is nursed back to health by a kind family. Eventually, he returns home, discovering 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 perpetuate the narrator's mind.