Towards the end of the nineteenth century, bizarre flashes of green light are witnessed coming from Mars. The unnamed narrator, a Journalist, is assured by the astronomer Ogilvy that there is no possible chance of life on Mars but the scientists of Victorian Britain are unaware that cold, inhuman intelligences have been greedily watching Earth from that world, and soon after a mysterious cylinder crashes to Earth in Horsell Common outside the town of Woking ("Eve of the War"). The cylinder draws a crowd of curious onlookers, particularly after it begins to unscrew. Bizarre, tentacled lifeforms emerge from the craft but, having difficulty in Earth's gravity, soon withdraw. A group of young men, overcome with curiosity, approach the cylinder — but as they approach a large funnel like object emerges and incinerates them with an invisible beam of energy. The Journalist flees to his home in terror as the military arrive to form a cordon around the cylinder. Everyone complacently believes that the Martians now pose no threat, but ominously a second cylinder can be seen landing that night ("Horsell Common and the Heat Ray").
Sounds of battle from the common can soon be heard, and the Journalist is soon horrified to realise that his home lies directly in the line-of-sight of the Martian weapons. A young artilleryman comes to the Journalist's house seeking shelter, and reveals that he is a survivor of a battle on the outskirts of the town between the military and the Martians, who have created large tripod fighting-machines to move around in. On learning that the second cylinder was seen heading in the direction of London, the Journalist is horrified to discover that his beloved, Carrie, is now in danger, and joins the Artilleryman to make his way to London. The two are separated during a Martian attack, where the military are routed and the Journalist gets his first sight of the Martian fighting-machines ("The Artilleryman and the Fighting Machine").
By the time the Journalist reaches London, Carrie and her father have disappeared from their home in the panic. Devastated, the Journalist is carried aimlessly along with the panicking crowds, tortured by worry over Carrie. After witnessing the destruction of the suburbs and the breakdown of society in the panic over the approaching Martians, the Journalist realises that his only hope of escape is a boat out of England. By the time he makes his way to the docks, the boats are full and escaping, but the Journalist by chance sees Carrie aboard one of them. Although she desperately attempts to reach him, before they can reunite the boat begins to depart ("Forever Autumn"). Before the refugee ship can escape, however, a group of fighting machines encounter it. The battleship HMS Thunderchild attacks the fighting-machines to buy the refugee ship time to escape, but although it manages to destroy one, the hopes of the remaining survivors are dashed when the other fighting-machines successfully sink the ship. More cylinders can be seen arriving, and the Journalist realises that the Earth now belongs to the Martians ("Thunderchild").
Trapped in England, the Journalist finds himself wandering through a bizarre landscape gradually transformed by the parasitical Red Weed, a form of vegetation native to Mars which gives it a distinctive red hue ("The Red Weed Pt. 1"). He comes across what appears to be the dead body of a parson in a churchyard and decides to bury him, but is stopped by the Parson's wife, Beth; the Parson, named Nathaniel, is alive, but has been deeply traumatised by his experiences. His faith shattered by the Martian invasion, Parson Nathaniel is convinced that the Martians are demons sent by God to wipe out humanity for its sins. Despite Beth's desperate pleas, Parson Nathaniel comes to believe that humanity is irredeemable and doomed, and he succumbs further to despair and insanity when Beth is killed after a cylinder falls on their house, trapping Parson Nathaniel and the Journalist inside ("The Spirit of Man").
Trapped in the house, the Journalist discovers that the Martians have been harvesting humanity and feeding on their blood. This prompts Parson Nathaniel to snap, and the Journalist is forced to subdue him to silence his rantings. Their struggle attracts a Martian to the ruined house, however, and while the Journalist manages to hide the Martian drags Parson Nathaniel to his death. Soon after, the Martians mysteriously abandon their camp, allowing the Journalist to escape, and he rejoices in his freedom ("The Red Weed Pt. 2"). Making his way back to London, the Journalist once again encounters the Artilleryman, who reveals that he has a plan to rebuild human civilisation in the drains and sewers underneath London. Although the Artilleryman's utopian visions temporarily sway the Journalist, he soon discovers how feckless and lazy the Artilleryman actually is and abandons him in disgust ("Brave New World").
Upon arriving in London, the Journalist discovers the city in ruins, covered in thick black dust. The city is full of solitary Martian fighting-machines emitting a pained howl; upon encountering one, the Journalist snaps and decides to sacrifice himself to it, but discovers birds feeding on the Martian inside and realises it is dead. ("Dead London"). Exploring further, the Journalist discovers a ruined Martian camp and realises that the Martians have been killed by bacteria native to Earth to which they have no immunity. Humanity begins to rebuild, and the Journalist is reunited with his beloved Carrie; however, the prospect of a further Martian attack in the future continues to cause concern ("Epilogue #1"). Years later, a NASA mission to Mars reports bizarre dust-storms and flashes of light from the surface before losing contact with Mission Control. The concerned administrator at the Jet Propulsion Laboratory in Pasadena tries to make contact with other NASA tracking stations, but one by one begins to lose touch with them... ("Epilogue #2")