In 1996, at the 45th-year reunion of the class of '51 at Weequahic High School in Newark, New Jersey, writer Nathan Zuckerman meets one of his old friends, Jerry Levov. They talk about Jerry's older brother, former all-state star athlete Seymour ('Swede'), class of '44, who recently died after a long illness.
The flashback shows a young Swede persuading his father, glovemaking magnate Lou Levov, to let him marry his high school sweetheart, New Jersey's 1947 Miss America contestant Dawn Dwyer. Lou is skeptical because Swede is Jewish and Dawn is a devout Roman Catholic, but her strength and honesty sways him. They have a daughter, Meredith ('Merry'), and settle in the town of Old Rimrock, where they acquire a large farm, with Swede commuting the 30 miles to the Newark glove factory.
Merry struggles with a stuttering problem, which her parents are unable to get a handle on – though Grandpa Lou says it is simply because her mind works so fast. Merry is smart and quirky, and is deeply affected as a 12-year-old by the self-immolation of Thích Quảng Đức in 1963.
By the time Merry reaches high school, she has become increasingly radicalized as the Vietnam War rages, and frequently goes to New York City to take part in antiwar protests. When Merry lashes out during the 1967 Newark riots, Swede urges her to channel her energy into protesting against the war from closer to home. A few days later, the town's little post office and store is destroyed by a bomb, killing the owner.
Merry disappears, and is the FBI's prime suspect, though Swede and Dawn believe she is innocent or, if involved, being forced to act by older radicals she met in New York. Swede searches for her, hounding the FBI for information, but she is not heard from.
Some time later, 22-year-old university student Rita Cohen presents herself at the glovemaking factory, ostensibly working on a report for business class. Rita tips off Swede with credible information about Merry, hints that she knows Merry's whereabouts, then asks him to meet her at a hotel with $10,000 cash.
Swede meets Rita in the hotel room, but spurns her mean-spirited attempts to seduce him. Rita runs off with the money and leaves no further information regarding Merry. Swede calls in the FBI, pointing to the Rita connection and the recent bombing in the Greenwich Village townhouse explosion, but the agency has no more use for Swede's inept interference.
The strain of Merry's disappearance eventually causes Dawn to have a nervous breakdown. After treatment, Dawn starts an affair with a neighbour, tells Swede that Merry has destroyed their former life, and tries to get Swede to forget about Merry so that they can start a new life. He refuses to stop looking.
In 1970, Swede spots Rita on a New York City street. Rita takes him to a skid-row area of Newark where Merry now lives. During two brief visits, Merry confesses to Swede that she made and planted a total of 3 bombs, killing 4 people.
She tells of how she later slid into the underground, where she was taken robbed and raped repeatedly. As a penance for her crimes, she has withdrawn from society, and is practicing extreme asceticism within the Indian religion Jainism (though the quietness of her physically dirty and simple life style has ended her stutter). She has no desire to return home, and says that if he loves her, he'll let her be.
We see the years pass in a series of shots of Swede growing older as he keeps returning to stand outside the abandoned house where he last found Merry. Swede never sees Merry again.
In the present, at Swede's funeral, Nathan muses that we know we are alive when we realize that 'all the time... we are wrong' about our assumptions 'about everyone'. As the mourners are leaving, a cleaned up middle-aged Merry arrives, silently passing her uncle and mother as she walks to Swede's grave.