The story is narrated by John Wheelwright, a former citizen of New Hampshire who has become a voluntary expatriate from the United States, having settled in Toronto, Ontario, Canada and taken on Canadian citizenship.
The story is narrated in two interwoven time frames. The first time frame is the perspective of John in the present day (1987). The second time frame is John's memories of the past: growing up in New Hampshire in the 1950s and 1960s alongside his best friend, Owen Meany.
Present day (1987)
The events of 1987 are related in the style of diary entries. The present-day John Wheelwright works as an English teacher at the Bishop Strachan private girls' school in Toronto. He is an Anglican, and although he feels a strong sense of religious faith, he also experiences doubts about Christianity. A virgin and a bachelor, John is fixated on his past life and the political conditions in America, in particular, the Reagan administration. John's present-day narrative punctuates his retelling of past events, providing commentary and more recent anecdotes.
John Wheelwright and Owen Meany both live in the fictional town of Gravesend, New Hampshire. The boys are close friends, despite the fact that John comes from a historical and wealthy family — as the illegitimate son of Tabitha Wheelwright — and Owen is the son of a working-class granite quarryman. John's earliest memories of Owen involve lifting him up in the air, which was easy due to his permanently small stature, in order to make him speak. A damaged larynx caused Owen to speak in a high-pitched shouting voice at all times. During the course of his life, Owen develops the conviction that he is "God's instrument".
As John and Owen move through their schooling, it becomes clear that Owen is advanced in his intellect and self-awareness. He expresses frustration with his parents, over whom he appears to have complete control, and favors John's mother and grandmother, choosing to spend the majority of his time at John's house on Front Street. John's mother, Tabitha, eventually marries a drama teacher from a local private high school, Dan Needham. Needham wins the affection of the boys by giving them a stuffed armadillo to play with; Owen is particularly taken with the creature, and he and John take turns playing hide-and-seek with it. Although John likes Needham, he and Owen speculate about who John's biological father might be — Tabitha refuses to tell him.
Owen is also fond of baseball; despite being a poor player, he curates an enormous collection of baseball cards. At a Little League baseball game, he unexpectedly gets up to bat and hits a foul ball, which strikes Tabitha in the head, killing her immediately. John is distressed, but he and Owen remain friends following a nonverbal exchange facilitated by Dan Needham. It is at this point that Owen reveals that he feels that he is an instrument of God. In order to express this to John, he removes the claws of the stuffed armadillo, just as God has metaphorically taken command of his hands. Later on, he appears as the baby Jesus in a Nativity production at the Episcopal Church he and John attend, and as Ghost of Christmas Yet to Come in a local performance of A Christmas Carol. During the latter role, he becomes convinced that he saw his full name and the date of his death on Scrooge's grave stone. These events reinforce Owen's ideas about his connection with God.
Because John is held back in school, Owen repeats the ninth grade with him so that the two can attend the Gravesend Academy together. There, Owen Meany earns a reputation as an intelligent, sarcastic student. He is known for his heavily opinionated editorial column in the school newspaper, in which he writes in all-capital letters to reflect his shrill voice; he also earns respect by dating John's college-age cousin Hester. While Owen helps John with his schoolwork, John assists Owen in practicing a basketball maneuver they call "The Shot". This involves John lifting Owen above his head so that he can dunk the basketball. Owen does not reveal why they must practice The Shot; it is not legal in any basketball game. However, they continue to rehearse the move so that they can complete it in under three seconds.
Due to a rivalry with the headmaster of Gravesend Academy, Owen is expelled in his senior year, squandering his chances of going to Harvard or Yale University, both of which had offered him full scholarships. Instead, he chooses to attend the University of New Hampshire while undergoing ROTC training so that he will graduate as a second lieutenant and assume active duty following graduation. This is received poorly by both John and Hester, who oppose the Vietnam War. Despite his insistence that he must join the military himself, Owen helps John to avoid the draft by slicing off some phalanges of his index finger.
Following graduation from university, Owen works as a casualty officer, bringing the bodies of Arizona soldiers home from California. This recalls his work carving and selling tombstones from his father's quarry. Eventually, Owen tells John and Hester that he has had a recurring dream in which he saves many Vietnamese children, but he sustains wounds that kill him. He believes that this will happen on the date he saw on Scrooge's grave, and he sets out to realize the dream by going to Vietnam. John and Hester are distraught, and attempt to convince Owen that it was only a dream. However, at this point, the novel flashes forward a few years to Owen's funeral, which confirms his premature death. At the funeral, Owen's father reveals to John that he considered Owen to be "like the Christ Child", due to the fact that he and Mrs. Meany never performed intercourse. He also tells John that he told Owen about his apparently immaculate conception when Owen was a young boy. In the flash forward, it is also revealed that John has discovered the identity of his father — a man whom he has known all his life. He is frustrated that it is Reverend Lewis Merrill, the meek married minister of the Gravesend Congregationalist Church.
The novel returns to a chronological sequence as John relates visiting Owen in Arizona as the predicted date of his death approaches. Owen delivers a body to a poor, dysfunctional family that expresses contempt for the military. At the wake, John accompanies Owen as he confronts Dick, the nihilistic, violent brother of the deceased soldier. Dick expresses a desire to kill Vietnamese people as he shows off the lethal weaponry his brother smuggled in from Vietnam. John and Owen then return to the airport, where Owen concludes that his dream was, after all, nothing more than a dream, as he has reached the date of his death and he is not in combat. However, a large group of Vietnamese children arrive at the airport, and Owen recognizes the circumstances of his dream immediately. Dick, whom John had seen skulking around the airport, attempts to murder the children using a grenade. John catches the weapon, and tosses it to Owen; together they complete The Shot maneuver in order to quickly remove the grenade from the vicinity of the children. The detonation fatally wounds Owen. As he dies, his voice and physique calm the frightened children. He dies satisfied that he has fulfilled the will of God.
John is left with the memory of his friend, and the firm belief that Owen and his life were a miracle. The last words of his narrative are an impassioned plea: "O God—please bring him back! I shall keep asking You."