The film begins with a voice (Sir Cedric Hardwicke) telling the audience that greedy eyes are watching the blue planet. They envy our water, clean air and plenty of resources. The race of beings watching the blue planet had considered moving to another planet in the Solar System but were unable because every other planet is uninhabitable. Also, it tells us that there has been a WWI and a WWII, but that there is going to be another kind of war, The War of the Worlds. At a time when the Earth and Mars were closest to each other in orbit, the Mars beings begin to attack.
A strange fireball streaks across the southern California skies and lands in a gully in the San Gabriel mountains east of Los Angeles. Firemen quickly extinguish the fire that has broken out, but authorities are puzzled by the long, cylindrical object that fell to earth and started the fire. The object attracts tourists--and also the attention of Dr. Clayton Forester (Gene Barry) of the Pacific Technical Institute. While everyone else regards the object as anything from a tourist attraction to a potential treasure trove, Forester knows that something is wrong: the object did not come down like an ordinary meteor, and was much more lightweight than any meteor ever reported. What's more, the object is not only hot, but also radioactive.
Forester stays in the nearby town at the home of Pastor Matthew Collins (Lewis Martin) and his niece, Sylvia van Buren (Ann Robinson). Three men are left in the surroundings of the object when a hidden lid on the cylinder unscrews, and a long-necked probe rises out. The three try to approach the probe, declaring their friendly intentions--and the probe spits out a heat ray that incinerates the men and starts another fire. At the same time, power and telephone service fails in town, and everyone at the social discovers that his watch has stopped. Forester determines that the watches have been somehow magnetized, and also notes that someone's pocket compass points not to the north, but to the meteorite. Forester returns to the site with the sheriff and another deputy. They find the ashes of the three men, and then the probe attacks again, killing the deputy as he tries to drive away. Forester then determines that they are dealing with something from another planet and need to call in the military, especially as another fireball lands nearby as he is talking to the sheriff. While everyone waits for the soldiers to arrive, Forester appears on a radio program and deals with the increasing speculation on the otherworldly origin of the cylinders. A consensus arises that the cylinders come from Mars, now at its closest approach to Earth.
Marines from El Toro Marine Base roll in and surround the site, and an Air Force plane drops a flare on it from above. The long-necked probe fires its heat ray at the plane, and then sweeps the area, destroying a radio truck. The Marine colonel calls for reinforcements, and the 6th Army Command arrives, with artillery and tanks. Major General Mann, the commander, tells Forester that other objects like the one they are surrounding have landed in cities all over the world, and that all communication fails after that. Then the probe rises again, and we now see that it is part of a swan-like magnetically levitating low-altitude craft. Two other such craft rise out of the cylinder to join it. The officers give the order to prepare to fire, but Matthew Collins objects, saying that no one has tried to offer them peace before. Disregarding his own safety, he walks toward the three metal swans, reciting the 23rd psalm--and before his niece Sylvia's horrified eyes, the lead swan burns him to death. At once General Mann (Les Tremayne) and Marine Colonel Heffner (Vernon Rich) give the order to fire.
The soldiers unleash a barrage of artillery and missile fire--and none of it is effective. The swans possess a magnetic force shield that deflects any bombardment. The swans quietly take the measure of their opponents and then start to return fire, with heat rays and meson-disrupting energy bursts that disintegrate anything they touch. Forester urges Mann to inform Washington that conventional military forces would be outmatched. Mann leaves, and Heffner fights a holding action before finally ordering a complete retreat--and being disintegrated in mid-order.
Forester takes Sylvia with him in an Army plane. Flying low to avoid the Air Force jets flying in to try their hand, he clips some trees and crash-lands. He and Sylvia barely have time to escape before a squadron of swans surround the plane. General Mann returns to the city, where skeptical reporters cannot believe his reassurances--and of course he knows better, because nothing has proved effective.
Alone in the brush, Forester and Sylvia take shelter in an abandoned farmhouse. There Sylvia confesses her fears and her deep sense of loss following her uncle's death. In the middle of this tender conversation, another cylinder crashes into the side of the house. Hours later, Forester wakes up, and a terrified Sylvia tells him that the house is surrounded. Forester works diligently to clear a way out, while also trying to observe as much as he can. The Martians lower a different kind of probe, an eye-like camera; Forester, at first taking this for yet another weapon, chops the camera head from its extender, which swiftly withdraws. A Martian crewman enters the house and touches Sylvia on the shoulder; Forester blinds it with a flashlight and then throws an axe at it, putting it to flight. When Forester realizes that he is holding a scarf now stained with Martian blood, Sylvia loses all control, and Forester has to shout at her to calm down. They then escape, just before the Martians burn down the ruins of the house.
As more cylinders come down all over the earth, the Martians' goal becomes painfully clear: to drive all of humanity before them and eventually to kill us all. In Washington, the Secretary of Defense prepares to order the dropping of an atomic bomb on the Los Angeles-area nest. Forester and Sylvia finally arrive at Pacific Tech and turn over the alien camera and the blood-stained scarf. The blood turns out to be anemic, and the camera yields little insight other than that the Martians perceive color a lot differently from humans and that their ability to see is hampered by bright light. At the time, Pacific Tech officials think all this is a moot point, because the atom bomb is going to stop them anyway. But even the atom bomb proves ineffective against the Martians' magnetic force fields.
General Mann, clearly frustrated, orders an evacuation of Los Angeles. Forester tells his colleagues that now the anemic blood is important, because only biological weapons will stop the Martians now. The plan is to take as many lab instruments as possible into the mountains and set up another laboratory. But that plan comes to nothing, as looters seize the Pacific Tech vehicles and scatter or beat up all the personnel, including Forester, the pathologist who found out about the anemia, Dr. Dupre (Ann Codee), and Sylvia. As the swans arrive and start systematically burning every building in sight, Forester rushes about, going from church to church, hoping to find Sylvia waiting there, as she once waited after running away as a child. He finds church pastors everywhere praying for deliverance, comfort, or both, and at one church he even finds two of his colleagues. At last he finds Sylvia--and as the two rush toward one another, a nearby swan burns out a stained-glass window, frightening everyone inside.
But the attacking swan abruptly heels over, fires only two more seemingly half-hearted bursts, and then crashes into a building and falls to the street. Dead silence descends. Inside the church, Forester leads the people out into the street to see what has happened. They find the downed swan, and as they watch, a door opens and a Martian arm appears, trying to move out. Another swan crashes on the other side of the street and, as Forester watches, the Martian arm turns a mottled gray and falls still. Forester touches it and pronounces it dead.
And in fact, this story is repeating itself everywhere. The Martians had very underdeveloped immune systems, and as soon as they were exposed to Earth's atmosphere, they became infected with germs that a humans have long since developed immunity to, but which proved uniformly fatal to Martians. The metal swans stop and fall where they are, and the invasion is over even more swiftly than it began.