Rachel Lapp (Kelly McGillis), a young Amish widow, and her 8-year-old son Samuel (Lukas Haas) are traveling by train to visit Rachel's sister. At the 30th Street Station in Philadelphia, Samuel inadvertently sees two men brutally murder a third. Captain John Book (Harrison Ford) is the policeman assigned to the case.Samuel witnessed the murder, a slashing, in the restroom and escaped the killers' detection by hiding in a stall. Book and his partner, Sergeant Elton Carter (Brent Jennings), question Samuel. He is unable to identify the perpetrator from mug shot photographs or a police lineup, but notices a newspaper clipping at the police station with a picture of highly regarded narcotics officer James McFee (Danny Glover) and recognizes him as one of the killers. Book remembers that McFee was previously responsible for a drug raid where evidence had mysteriously disappeared from the police department.Book confides his suspicions to his superior officer, Chief Paul Schaeffer (Josef Sommer), who advises Book to keep the case secret so they can work out how to move forward with it. As Book returns home, he is confronted by McFee in a parking garage and badly wounded in the ensuing gunfight before McFee escapes. Since only Schaeffer had been told, Book realizes Schaeffer must have warned McFee and is also corrupt.Book calls Carter and orders him to remove the Lapp file from the records. Book then hides his Dodge and uses his sister's VW to return Rachel and Samuel to Lancaster County. After the Lapps' safe arrival in rural Pennsylvania, Book collapses from loss of blood in his vehicle in front of the Lapp farm.Impressing upon them that hospitalization will allow the corrupt officers to find him, Book is gradually tended back to health by the Amish. As Book heals, he begins to develop feelings for Rachel. The Lapps' neighbor, Daniel Hochleitner (Alexander Godunov) had himself hoped to court her and this becomes a cause of friction. Later Rachel and John are caught dancingan affront to the conservative Amish way of life. Rachels father-in-law, Eli, takes her aside and warns that if she continues she could be shunned (ostracized) by the community. Rachel, in turn, feels she has done nothing wrong.The corrupt officers intensify their efforts to find Book, who is informed via a call from a payphone that Carter has been killed. While still in town, Hochleitner and the other Amish men are harassed by local punks. Breaking with the Amish tradition of nonviolence, Book retaliates. The fight gets noticed by the local townspeople and is reported to the police. The news reaches Schaeffer.John subsequently comes upon Rachel as she bathes, and she stands half-naked without shame before him. He walks away without a word. Soon after, the two realize they are in love, but because of the publicity the fight has gotten, Book knows he must leave. Upset, Rachel removes her bonnet, and she and John run to one another, embracing with a passionate kiss.McFee, Schaeffer, and "Fergie" Ferguson (Angus MacInnes), the second killer at the train station, arrive at the Lapp farm with pump action shotguns. Book, unarmed and in the barn with Samuel, orders Samuel to run to the neighbors for safety. The trio split up and search for Book. John tricks Fergie into the corn silo and suffocates him under tons of corn. He retrieves Fergie's shotgun and kills McFee. A crazed Schaeffer then forces Rachel and Eli out of the house at gunpoint; Eli signs to Samuel (who returned unseen upon hearing gunfire) to ring the warning bell. Although Schaeffer briefly forces Book to surrender to him, the loud clanging summons all other Amish within earshot. With so many witnesses present it is clear to Schaeffer that he cannot escape, and he gives up.As Schaeffer is taken by local police and Book prepares to leave, he shares a quiet moment with Samuel, then exchanges a silent, loving gaze with Rachel. Eli bids Book goodbye for his return to Philadelphia, saying "You be careful out among the English [i.e., non-Amish]", as he had said to Rachel at the beginning of the film, and showing Book that he now respects him like the people of his own faith. As Book drives away from the Lapp farm, he passes Hochleitner, presumably on his way to court Rachel, and exchanges an amicable wave of farewell.