In 1984, an Amish community outside of Lancaster, Pennsylvania attends the funeral of Jacob Lapp, who leaves behind a young wife Rachel (McKillis) and eight-year-old son Samuel (Haas). Rachel and Samuel travel by train to visit Rachel’s sister, which takes them into Philadelphia. While waiting at 30th Street Station for a connecting train to Baltimore, Samuel goes into the men’s room and witnesses the brutal murder of an undercover police officer, but manages to evade detection by hiding in the stalls.
Detective John Book (Ford) is assigned to the case where he and partner Sergeant Elton Carter question Samuel. Although Samuel is unable to identify the perpetrator from mug shots or a lineup, he later sees a newspaper clipping in a trophy case of narcotics officer James McFee (Glover) receiving an award and points him out to Book. Book investigates and finds out that McFee was previously responsible for a seizure of expensive chemicals used to make black-market amphetamines, but the evidence has now disappeared. Book surmises that McFee himself fenced the chemicals to drug dealers, and that the murdered detective, Ian Zenovich, had been investigating the theft.
Book expresses his suspicions to Chief of Police Paul Schaeffer, who advises Book to keep the case secret so they can work out how to move forward. Book is later ambushed and shot in a parking garage by McFee and left badly wounded. Since only Schaeffer knew of Book’s suspicions, Book realizes Schaeffer is also corrupt and tipped off McFee. Realizing that Samuel and Rachel are now in grave danger, Book orders his partner to remove all traces of the Lapps from his files, and drives the boy and his mother back home to Lancaster County where they could disappear within their community. While attempting to return to the city, Book’s loss of blood causes him to pass out in the vehicle in front of their farm.
Rachel argues that taking Book to a hospital would allow the corrupt police officers to find him and put Samuel in danger. Her father-in-law Eli reluctantly agrees to shelter him despite his distrust of the outsider. Book slowly recovers in their care and begins to develop feelings for Rachel, who likewise is drawn to him. The Lapps’ neighbor Daniel Hochleitner had hoped to court her, and this becomes a cause of friction.
During his convalescence, Book dresses in Jacob Lapp’s former clothing in order to avoid drawing attention to himself. His relationship with the Amish community deepens as they learn he is skilled at carpentry and seems like a decent, hard-working man. He is invited to participate in a barn raising for a newly married couple, gaining Hochleitner’s respect. However, the attraction between Book and Rachel is evident and clearly concerns Eli and others, causing much gossip in the tight-knit community. That night Book inadvertently observes Rachel bathing, but as she stands half-naked before him, he walks away.
Book goes into town with Eli to use a payphone, where he learns that Carter has been killed. He deduces that Schaeffer and McFee murdered Carter after discovering his role in the case to get closer to Book, with the aid of a third corrupt officer, Ferguson. In town, Hochleitner is harassed by locals. Book retaliates, breaking with the Amish tradition of non-violence. The fight between the bullies and the strange “Amish” man is reported to the local police, who then inform Schaeffer, who had previously contacted the sheriff in his efforts to locate Book, Rachel and Samuel.
The next day, the corrupt officers arrive at the Lapp farm and search for Book and Samuel, taking Rachel and Eli hostage. Book orders Samuel to run to Hochleitner’s home for safety, then tricks Ferguson into the corn silo and suffocates him under tons of corn. He retrieves Ferguson’s shotgun and kills McFee. Samuel, hearing the gunshots, heads back to the farm. Schaeffer then forces Rachel and Eli out of the house at gunpoint; Eli signals to Samuel to ring the farm’s bell. Book confronts Schaeffer, who threatens to kill Rachel, but the loud clanging from the bell summons the Amish neighbors, who resolutely gather near and silently watch him. With so many witnesses present, Schaeffer realizes he can’t kill them all nor escape, and gives up; Book takes Schaeffer’s guns before he is arrested.
Book says goodbye to Samuel in the fields as he prepares to leave; he and Rachel share a long loving gaze on the porch. Eli wishes him well “out there among them English” signifying his acceptance of Book as a member of their community. Book smiles and departs, exchanging a wave with Hochleitner on the road out.