During the day on Halloween, Johnny concocts a bioluminescent formula by the river. When his dog, McDuff, runs off, Johnny meets wheelchair-bound Steve and his brother Paul. The three boys bond over Johnny’s experiment, but as they leave, a hobo emerges from the shadows and discusses the need to relocate Rakia, which turns out to be a Bulgarian moonshine.
Johnny visits Ben, the school handyman and his friend. The two talk about inventing and helping people, as well as God’s omniscience. Johnny comes close to telling Ben about owning a healing cloth, which was willed to him by his grandfather, along with a whole trunk of interesting objects. (In the last book, the cloth healed McDuff.) But Johnny changes his mind and doesn’t.
Meanwhile, Professor Karl Mangle, an old friend and colleague of Harold Whittaker who is Johnny’s father, searches desperately for the miraculous cloth. He wants to heal his ill son, Steve, whom Johnny previously met.
Johnny’s friend Emmy urges him to persuade his father to let him come trick-or-treating with her. Johnny goes to Duke University to talk to his father, who works as a professor there. On his way, he’s sidetracked by the scientific elements in Mangle’s office. Johnny hides behind a door when Mangle and his father enter and discuss religion and science. Johnny is able to slip out of the room before they notice him.
Johnny then meets his father in his own office. Johnny asks him to translate his grandfather’s journal, which came from the same trunk as the healing cloth. His father agrees. Johnny also asks to go trick-or-treating. Harold grants Johnny permission to accompany his friends.
While his father answers his phone, Mangle introduces himself to Johnny and invites him to visit his boys at their home that evening. Once Mangle leaves, Harold warns Johnny not to tell anyone about the journal or the cloth.
The Whittaker family prepares to welcome trick-or-treaters themselves. Johnny gives his father the journal before joining Emmy for the evening. A hobo turns up at their door asking for a meal, which Mrs. Whittaker gladly prepares for him.
Johnny and Emmy pick up Paul and Steve. Johnny learns that muscular dystrophy keeps Steve wheelchair-bound. The kids run into two bullies but are able to get away from them. Later, they think the bullies are in the abandoned Granville house. The kids decide to scare them.
At the Granville house, the weight of Steve’s wheelchair is too much for the rotted floor. It breaks, and the kids all fall through it into a crawl space that is only a few feet below the floorboards. Before lifting Steve out and leaving, Emmy and Johnny see a hidden coffin with a boot sticking out of it deeper in the crawlspace. The kids don’t tell their parents and decide to meet that Saturday to discover what lies under the floorboards.
After a disagreement that night with his father, Johnny skips school the next day to mull over his frustrations. He goes to the riverbank to think, but Fiona, his stepmother, receives a call from school informing her that Johnny was absent. She talks to him about his frustrations. That night, unable to sleep, Johnny sneaks into his father’s study, a place where he’s forbidden to go, and reads a translated account of a miraculous dream and experience that church Father Lucian had involving a miraculous cloth.
Hoping to discover if this cloth and his cloth are connected, Johnny unlocks the place where his father keeps their family Bible, which is stuffed with notes and letters, and begins to read. Charlie, his younger half-sister, interrupts him, and he must put everything away carefully.
The next morning, Saturday, Johnny lies about having been in his father’s study the previous night. Later, after noticing how quiet Johnny is, Fiona, tells him that God can use anything for good. Johnny decides to test the truth of her statement by bringing the miraculous cloth to the Granville house that night to heal Steve.
As John and Emmy make their way to the Granville house, they meet Paul, who informs them that his mother took Steve to the hospital and that he no longer wants to explore the old crawl space. Johnny and Emmy still want to explore it.
The kids barely make it into the crawl space with the coffin before they hear two voices —Mangle’s and the hobo from Halloween — talking about the need to move Rakia again because the kids discovered their hiding place in the crawl space. The kids assume Rakia is a woman’s name, and those talking murdered her.
Johnny and Emmy tell Ben about the crawl space and the Rakia. Ben asks them not to continue investigating. He promises to look into everything.
Though Steve ought to have come home after a brief stay in the hospital, the doctors diagnose him with double-lung pneumonia and keep him for a longer period. When he finally recovers enough to receive visitors, Johnny puts the healing cloth on him. He is disappointed when Steve isn’t healed. But Steve reassures him. He believes his illness isn’t an accident, and God will use it for good.
The next Sunday after church, Johnny and Emmy are conducting an experiment outside when they see the hobo and the soda shop owner following Ben. The hobo is carrying a gun.
When they hear a shot, they rush to help. Ben falls to the ground and is unresponsive. He is bleeding. Emmy runs to get help, and Johnny tells the hobo to press the healing cloth against Ben’s chest, as it is the only thing he has that will staunch the flow of blood. Mangle comes out of the woods, and the three men confess, not to a murder, as Johnny suspects, but to the illegal production of Rakia to supplement their incomes and help with Steve’s medical bills.
Suddenly, Ben wakes up. He has a bullet hole in his shirt but otherwise no sign of injury — not even a wound to explain the blood. As Johnny makes his way home, he can’t explain why the cloth seemed to heal McDuff and Ben but didn’t help Steve.
Johnny’s father greets him and congratulates him on being a hero, explaining that the police phoned and informed him of how Johnny had uncovered the Rakia plot. He has not yet determined whether he should punish John.
The next Sunday, Fiona takes Johnny for a horse ride, and Johnny realizes that Fiona has become a true mother to him. He discusses his biological mother’s passing with her. Fiona tells Johnny about the importance of faith and trust in God. Johnny accuses her of not understanding what it’s like when God takes something or someone important away from you. Later, as they race their horses, Fiona crashes into a protruding branch from an elm tree. The accident causes her to lose her sight.
Harold comes to Johnny with the translation of his grandfather’s journal about the healing cloth. He is excited that the journal says the cloth is in the trunk that belongs to Johnny. He asks Johnny to get the cloth. Johnny rushes to the shed where he stuffed the cloth for safekeeping and discovers that it’s gone.