Ray is a depressed man. He has two kids, Robbie and Rachel, who hold little respect for him. He works for a docking company. His boss is an overweight, stubborn man named Sal. He is a survivor to the martian attack on Earth.
A Tripod landed in his neighbourhood via lightning storm and totally destroyed it. But Ray and his children escaped in a working van. Ray witnessed the demise of his three close friends Manny, Vincent, and Julio. They then moved to Mary Ann (Ray's ex wife) and Tim's (Mary Ann's new husband) house, but they were not there. That night they slept in the basement and a plane crashed nearby, extinguishing most life in the neighbourhood.
In the morning, Ray went to investigate the crash and met Max, a deaf man who was the cameraman for a news team. Max led him to the head of the team, a news producer, who told Ray that there was more than one tripod and that they were on other continents. Additionally, she revealed that they were piloted by invaders from space. Ray got his children and drove to the Hudson River Ferry so they could get to Boston, where Mary Ann and Tim were. At the Hudson River Ferry, they learned that there was no information about the rest of the world and that society had collapsed. Ray's van was taken by an armed man, who was killed shortly afterward by a mob of people. Ray and his children then go to the ferry on foot, and meet a friend of Ray's, Cheryl and Laura. Several tripods attack and Ray is seperated for Cheryl and Laura, but he and his children reach the ferry. Another tripod, however, was under the water and remained unseen, but surfaced, knocking the ferry into the water, and tripods began to harvest people from the ferry. Ray and his children escape, again, and join a herd of refugees moving (presumably) towards Boston.
While moving through a countryside, the refugees see a large battle taking place. Some refugees keep moving, but others want to see the tripods get destroyed and go over to see it. Ray knows (from the news producer) that the tripods have a shield and are nearly impervious to attack, and knows that anyone going over the hill will probably die. Robbie, however, runs up the hill to assist army forces. Ray leaves Rachel and goes to find Robbie. He does, and tries to get Robbie to come with him, but Rachel is going to be taken by a family of well meaning people who think that she has been abandoned and Ray must choose between his children. He decides to help Rachel and when he comes back for Robbie, Robbie is gone. A gigantic explosion then takes place incinerating the other side of the hill, which Robbie (seems) to be on. Some humvees escape, though, and Ray holds hope that Robbie escaped with them.
Ray and Rachel hide in a farmhouse that a man named Harlan Ogilvy is hiding in. Ogilvy has lost his entire family to the tripods and is seething with a need for revenge and has possibly become deranged. Over the next several days, Ogilvy explains to Ray his plans for a resistance movement and also informs Ray that through unknown means, the Japanese have defeated the tripods. After hiding from a tripod's camera and the aliens inside a tripod, Ray becomes wary of Ogilvy, who has almost caused he and Rachel's deaths several times. They discover Red weed growing and see what aliens do with captives: Use their blood as fertilizer for red weed. Ogilvy becomes completely insane and Ray is forced to kill him. He and Rachel then drift into a deep sleep.
They wake up with a Tripod's camera watching them. Rachel panics and runs out of the basement and is taken by a tripod. Ray finds some hand grenades from a wrecked humvee and, having nothing left to live for after losing his children, attacks the tripod. The tripod notices him and picks him up in its basket. He discovers Rachel and, with the help of a captured soldier, manages to destroy the tripod with his remaining grenades. Ray, Rachel, and the others from the basket then press on towards Boston.
After meeting up with another stream of refugees being assisted by soldiers, Ray and Rachel enter Boston and see that the red weed is dying, and a tripod died on its own. Ray sees a tripod and notices that its shield is down and informs the soldiers, who kill it quickly. Ray and Rachel move on towards Mary Ann's parents' house, and meet Mary Ann, Tim, Mary Ann's parents, and Robbie, who miraculously survived the massacre on the hill. What happens next to Ray is unknown, but possibly he has decided to stay in Boston to be as close to his children as he can be.