The novel opens in 1951 when Reuben Land is born with faulty lungs. It is his father, Jeremiah, who miraculously and heroically saves his life. Reuben, the eleven-year-old narrator, explains that his father performed several true miracles in his lifetime, the first of which was bringing Reuben to life. Jeremiah is an extremely religious single father who lives with his eldest son Davy, Reuben the middle child, and his youngest and only daughter Swede.
The Lands lead a calm life until Jeremiah, the school janitor, prevents the town's bullies, Israel Finch and Tommy Basca, from attacking Davy's girlfriend in the school locker room. While on a hunting trip to Jeremiah's old friend August's house in North Dakota, Davy sulks away from Jeremiah and Reuben tries to prove that he is old enough to shoot. When they return home, they find that their front door has been tarred, presumably by Basca and Finch.
One evening Jeremiah takes Reuben to the new church he has been attending. Reuben skips out of most of the ceremony to spend time with his crush, Bethany Orchard, and when he returns to the church he finds several people including his father speaking in tongues and writhing on the ground. When the two return from church, they find that Swede has just returned from being briefly kidnapped by Basca and Finch. They celebrate her 9th birthday the next day and try to distract her with Western-themed gifts. Lurvy, a traveling salesman and friend of Jeremiah’s, interrupts their dinner, greedily eating all Jeremiah's specialty soup. Surprisingly, however, they never run out of soup.
Some time after Swede's birthday, Reuben wakes up in the middle of the night to two people breaking into their house. Davy, also awake, warns Reuben to remain quiet before shooting Israel Finch and Tommy Basca, the two intruders who intended to harm Davy.
Life for the Lands quickly deteriorates; Davy goes to jail before his trial and Jeremiah is fired from his job. For the trial, the Lands stay with their lawyer, Mr. DeCuellar, and his wife. Reuben testifies and realizes that Davy is not going to win. Swede and Davy concoct a plan to break Davy out of jail but they fall asleep and when they wake, the siblings find out that Davy escaped on his own.
The Lands wait to hear about Davy's escape, first on horse, then hitchhiking his way to August's before borrowing a car and leaving for some unknown destination. The police and a federal investigator named Andreeson press the Lands for information and encourage them to turn in Davy if he makes contact. Jeremiah, based entirely on faith that he will find his son, decides to sell the house and pursue Davy in the mobile home that he inherited from the now dead, Lurvy.
Jeremiah, Reuben, and Swede pack up all of their things and head West for August's house. They learn that Andreeson has been by and he is likely following them, but no one knows where Davy is headed. While they are stopped in a small town in North Dakota, Andreeson approaches them and Jeremiah rebukes everything the fed has to say. Swede secretly sabotages Andreeson's car and the family is able to escape from him. They travel for hours without stopping at a gas station because they are all manned with police officers looking for the Lands. Miraculously, they do not run out of fuel and they are never spotted, despite the distinct mobile home.
Finally, they pull into a gas station in the Badlands. Roxanna Cawley runs it; she invites them to stay in her home and wait out the snowstorm. The Lands resume a somewhat normal life at Roxanna's; Jeremiah recovers from pneumonia and begins to court Roxanna. Andreeson appears from time to time and eventually Jeremiah gives in to the officer's requests for help looking for Davy, as it appears that Andreeson just wants to get Davy back.
One day while he is near the barn, Reuben sees a horse rider and knows instantly that it is Davy. Despite his troubled lungs, Reuben hikes up the snowy hill and is reunited with his brother. Davy reluctantly agrees to show Reuben where is living that night. A man by the name of Jape Waltzer owns a small cabin with a young girl named Sara that he intends to marry once she is old enough. He has taken in Davy, which was kind, but he is a cruel man and the antithesis of Jeremiah. Reuben is conflicted about telling anyone about Davy's whereabouts, but Davy makes him promise to keep it a secret.
Andreeson, hot on the case, goes missing during a snowstorm and Reuben knows that Waltzer probably lured the federal agent away from town to kill him and so Reuben tells Jeremiah. A search party attempts to find Waltzer and Davy, but nothing comes of it. The Lands and Roxanna move back home and purchase the red farm where Jeremiah and Roxanna are married. Life returns to normal until Davy shows up one night with Sara in a car he stole from Waltzer. The family reconnects that night, knowing that Davy will have to leave the following day.
As Davy prepares to leave, Waltzer appears and shoots both Jeremiah and Reuben. As the commotion continues, Reuben describes a beautiful meadow where he and Jeremiah meet, presumably heaven. Reuben wakes up to find himself alive, Jeremiah dead, Davy escaped, and Waltzer never to be seen again. The narrative jumps forward in time, explaining that Roxanna continued to raise them and Sara stayed on the farm. Swede, with her flair for drama and love of literature, became a famous writer, Davy remained hidden in Canada, and Reuben happily married Sara.