Ray Ferrier (Tom Cruise) is a divorced union container crane operator with few skills as a father. Ray's ex-wife (Miranda Otto) drops off their rebellious but coming of age teenage son Robbie (Justin Chatwin) and meek 10-year old daughter Rachel (Dakota Fanning) for a weekend visit with their father in New Jersey. Ray is a self-absorbed individual who feels imposed upon by having to baby sit his own children. Then something happens that will change their entire lives. An unusual and violent lightning storm hits the town. In the intersection down the street, Ray sees a huge three-legged war machine rise from beneath the street. The machine begins to fire and incinerate everything and everybody. The Martians have begun the war by attacking Earth with only one goal in mind, destroying everything in sight. Ray becomes a real father when he decides to protect his children and take them to their mother’s house. Ray grabs his handgun and a few supplies and steals a minivan from his friend’s service station, begging the friend to come with them, but leaving him behind when he doesn't understand the danger and refuses to get in. The mother and her new husband have already left for Boston so the Ferriers hole up in their house. Overnight, the Martians show up around there and cause great destruction. A news van is outside and the reporter informs Ray the Machines are in all cities. They decide to try to make it to Boston. They start running for their lives and are just ahead of the Martians, when they get caught up in a frantic mob of people in upstate New York, who are also fleeing the machines. The mob tries to get in the car or take it away from them. In a Mexican standoff, Ray relinquishes the car to an armed gunman in exchange for letting him get Rachel out of the car. Ray drops his gun which is picked up by another mob member who shoots the other gunman. They manage to get on a ferry as several more machines rise in the distance and the ferry leaves before it's full. A machine rises from the river and overturns the ferry but the Ferriers swim to shore. Robbie follows an Army unit into battle against Ray's wishes but he cannot stop him. Ray and Rachel are taken in by a sole man holed up in the basement of his rural house. Machines are all around and they send a camera tentacle into the basement where they are holed up to look for humans whom they avoid by moving and hiding. Then some Martians come in personally to investigate, but they're called back to the ship before they find the humans. Ray and the homeowner dispute over how to handle the situation. The machines have increased in number and are everywhere, and they cannot be destroyed by our military. They make it to Boston and the Martians start dying from various sicknesses caused by germs that humans have built up immunity to, but the Martians don't have.