In 1936, Abilene Tucker moves to Manifest, a small town in southeast Kansas. She cannot stay with her father, Gideon Tucker, as he works on his railroad job in Iowa, so Gideon sends her to his childhood hometown for the summer. Abilene carries only a few belongings with her, and her most prized possession is her father's broken compass. Abilene jumps off the train a minute early so she can explore the outskirts of the town before she is officially introduced to everyone. As she walks into town, Abilene meets Shady Howard, the local pastor, who was supposed to meet her at the train station.
Abilene is disappointed to see that Manifest seems drab and lifeless in contrast to the vibrant town her father had described to her. She and Shady Howard walk into the newspaper offices of the local paper, Manifest Herald. There Abilene meets Hattie Mae Macke, a woman whose newspaper articles she has read. Hattie Mae lets Abilene select a few newspapers from 1917 to take with her and read while she is in town. Abilene is interested in newspapers from this year because it was a time when her father was young and still living in Manifest.
Abilene stays in Shady's home. When Abilene pulls up a floorboard in her room in order to hide her valuables, she finds that there is already a box sitting in the hiding place. The cigar box is full of neatly folded papers, but she has to wait for daylight to actually see the contents of the box.
Abilene attends the last day of elementary school in Manifest, then goes home to Shady's property. With the cigar box in hand, she climbs into a treehouse in his backyard. Inside the box, she finds a hand-drawn map and some letters dated 1918. The letters are sent from someone named Ned Gillen and addressed to someone named Jinx.
Two girls, Lettie and Ruthanne, visit Abilene in her treehouse, bringing sandwiches and Coca-Cola to share. The three girls strike up a friendship as they look over the old map and speculate about whether it might be a spy map from World War I.
They walk around town together and explore the woods, but as her friends go home, Abilene realizes that she has lost the compass her father gave her. She thinks she lost it while walking through the town cemetery, so she goes back to look. Next to the cemetery is a spooky house known as Miss Sadie's Divining Parlor. Abilene sees her compass hanging near the porch of the house, among a row of wind chimes. Abilene is startled when she sees a person on the porch, and she runs away without getting her compass, knocking over a clay pot in the process.
The next day, Abilene returns to retrieve her compass. She meets Miss Sadie and asks her for information about her father, Gideon. When Miss Sadie asks for a trinket belonging to Gideon, Abilene instead shows Miss Sadie the cigar box full of mementos from the past. Miss Sadie begins divining and telling Abilene a story about two boys. The point of view of the story shifts to 1917, as seen through the eyes of the boy named Jinx, to whom the letter in Abilene's possession is addressed.
In 1917, Jinx sees an older boy named Ned Gillen trying to convince a girl to go to the homecoming dance with him. Jinx is a hungry 13-year-old drifter, and he offers to sell Ned some special water to make himself smell good if Ned will give him the catfish he just caught. Jinx has an unknown secret in his past, which involves a dead body. He thinks that the death was not his fault, but he is still concerned that he will be caught by a sheriff and charged with the crime. Jinx and Ned have both finished bathing in the river and are in their undershorts when unknown assailants steal their clothes and use them to start a fire. The men who stole their clothes are wearing white hoods and white sheets. Ned tells Jinx that these men are dangerous members of the Ku Klux Klan. From their hiding place in the bushes, Ned identifies one of the men as Arthur Devlin, the boss of the local mine. Jinx and Ned put on a pair of white costumes they find near the gathering. Jinx pulls a prank on the Klansmen by leaving poison ivy leaves in place of newspaper in the outhouse that all the Klansmen are using.
Back in the present, Abilene is unimpressed with Miss Sadie's story about Jinx and Ned. It seems that the presence of a fishing lure helped Miss Sadie invent the story. Miss Sadie reveals that Abilene broke a priceless clay pot of hers the day prior, and the two of them strike a deal. Miss Sadie will return Abilene's compass to her if Abilene helps Miss Sadie with chores around her property. Miss Sadie has a festering wound on her leg and can use the assistance.
The next day, as Abilene works in her garden, Miss Sadie narrates another tale about the past. In 1917, Jinx waits for Ned to emerge from his job in the Devlin Coal Mine in Manifest. Jinx has been living with Shady Howard for three weeks now, and he is attending school and has become best friends with Ned Gillen. Many immigrants work in the mines, and Arthur Devlin, the racist owner of the mines, keeps the workers divided by nationality so that the different groups never interact. Jinx sees a notice outside the mines that warns American citizens that German or Austrian immigrants may be spies for their World War I enemies.
Jinx tells Ned a story about his criminal past. Jinx used to travel with his uncle, Finn, a skilled conman, until one day Jinx discovered that his uncle had killed a man. In Missouri, Finn kills another man, then knocks Jinx unconscious and leaves a bloody knife in his hand to make it look as if Jinx killed the second man. Ned assures Jinx that the accident was not his fault.
Abilene reads a letter sent from Ned to Jinx in February, 1918. Ned has joined the Army a year early by spending $25 to bribe a recruiting officer. Ned is now in training, about to be shipped out to fight in France. Miss Sadie continues the story after the letter ends, telling Abilene that life was difficult for Jinx after Nate shipped off. Jinx spends his summer doing odd jobs and fishing, but he hears that Uncle Finn might still be on the run from the police. Jinx himself is wanted on suspicion of murder, but he does not think that anything bad can happen to him in Manifest.
In June of 1936, Miss Sadie tells Abilene about how the coal mine owner, Arthur Devlin, wanted to buy a piece of property in the summer of 1918. The piece of property is likely a rich source of coal, but the land belonged to the recently deceased Widow Cane so Mr. Devlin can't buy it. The widow had no heirs, so her estate is in holding. The townspeople of Manifest realize that if they jointly purchase the land Mr. Devlin wants, they can use the property as a bargaining chip to ensure better working conditions for all the miners. The townspeople ask Jinx to help them come up with a plan to raise $1,000 to buy the property.
In August of 1918, Spanish influenza begins to spread in Manifest. The town is placed under quarantine, and no one may leave or enter town. Mr. Devlin leaves town before the quarantine begins. It is revealed that the quarantine is only a ruse, and the citizens of Manifest are merely faking the disease in order to continue with their plan to buy Widow Cane's property. The entire population of Manifest works to make a special kind of bootleg whiskey, which is mixed in the baptistery of the First Baptist Church.
In 1936, Abilene looks in a dictionary and learns that the word manifest can mean a list of passengers on a ship. She finds this fact significant because most of Manifest's citizens were immigrants who came to America on boats. The second definition for manifest is a verb which means to reveal. This definition also seems important because many things about Manifest have been revealed to Abilene through old newspaper articles, Ned's letters to Jinx and Miss Sadie's stories. However, Abilene feels there is so much about Manifest's history that remains hidden from her. She wants to know her father's exact connection to the town and why he decided to send her to live in the place.
In September of 1918, the bootleg elixir made by Manifest begins to sell very well because there are medicinal ingredients mixed in with the alcohol. Other cities are actually suffering from Spanish influenza, and the combination of liquor and medicine in the elixir helps sick people recover. By October, Mr. Devlin has returned to town, and all the miners must return to work. The townspeople are still $260 short of their $1,000 goal, but due to some quick thinking by Jinx, the townspeople are able to fool Mr. Devlin's assistant into buying a useless portion of the property. The townspeople of Manifest are then able to buy the important part of the land.
In late October of 1918, the townspeople are preparing to celebrate homecoming. Jinx's Uncle Finn finds him, and when Jinx refuses to rejoin his uncle in a life of crime, Finn shoots Jinx. Jinx receives a bullet wound to the shoulder, but survives. Then Finn's foot is caught in a raccoon trap, and he falls, hits his head on a rock and dies. A letter arrives in town, saying that Jinx's friend Ned Gillen has been killed in action in the war. The loss of Ned impacts Jinx worse than his own bullet wound.
In 1936, Abilene learns that Jinx was in fact her father, Gideon Tucker, and that he felt horribly guilty for Ned Gillen's death because he had helped Ned raise the money to bribe the recruiting officer to let him join the Army. Abilene also learns that a true plague of influenza hit Manifest in late 1918, and that this disease killed many of the characters she had grown to love from Miss Sadie's stories. Abilene begins to wonder whether her father will ever come back for her. Abilene goes to visit Miss Sadie again, and this time Miss Sadie allows Abilene to lance out the festering infection from the wound on her leg.
Miss Sadie reveals that Ned Gillen was actually her son. Circumstances separated them, and by the time Miss Sadie found him again, Ned had been adopted by a man in Manifest. Miss Sadie moved into town and loved her son from a distance, without telling him her identity.
In August 1936, the town of Manifest prepares for another homecoming celebration. Abilene sends a telegram to her father, asking him to come home. Gideon complies and embraces his daughter when they meet. They are going to remain in Manifest, and Abilene decides that she is going to take up reporting for the local newspaper.