Writing from his home in Toronto, Canada in 1987, John Wheelwright narrates the story of his childhood. Peppering his narrative with frequent diary entries in which he chronicles his outrage against the behavior of the Ronald Reagan administration in the late 1980s, Wheelright tells the story of his early life in Gravesend, New Hampshire, when his best friend was Owen Meany, who he remembers as the boy who accidentally killed Wheelwright's mother and made Wheelright believe in God. The narrative of A Prayer for Owen Meany does not follow a perfect chronology, as John pieces together the story he wants to tell.

Owen is a bizarre child. A tiny dwarf, he has weirdly luminous skin and an ethereally nasal voice (represented in the novel in all-capital letters). He has a tremendous crush on John's mother, who, in turn, is very fond of him; she even intervenes with Owen's parents to ensure that he will be able to attend the elite Gravesend Academy for high school. John does not know who his father is, though he does know his heritage: he comes from the aristocratic Wheelwright family. Owen's parents, in contrast, are undistinguished parents who run a struggling granite quarry. Nonetheless, Owen assures John that God will help him discover the identity of his father. John has always believed that his mother will tell him one day, but this hope is dashed; one day at a Little League game, Owen, ordered to bat for John, hits a high foul ball that falls onto John's mother's head, breaking her neck and killing her. John, brokenhearted, now splits his time between his grandmother's manor at 80 Front Street and his stepfather Dan Needham's apartment at Gravesend Academy, where Dan serves as a history and drama professor. John loves Dan, who becomes like a real father to him.

John and Owen remain close friends. In December, 1953, six months after John's mother's death, John begins to realize just how remarkable Owen is. Simultaneously, Owen wins the role of the Baby Jesus in the Episcopalian Christmas pageant and the role of the Ghost of Christmas Yet to Come in an amateur theatrical production of A Christmas Carol. Owen brings the Christmas pageant to a halt when he accosts his parents in the middle of the performance, demanding that they leave. He is chillingly good as the scary ghost in A Christmas Carol, but on the night of the final performance, he has a vision in which he believes he sees his own gravestone--complete with the date of his own death.

Over time, as more and more details of his death are revealed to him, Owen comes to believe that he is God's instrument on Earth, and that he is destined to die heroically. He even believes that God caused him to kill John's mother--he believes that he accidentally interrupted the Angel of Death when it came to take her, and as a result, he was forced to do the job himself. Inscrutably, he begins to make John practice something called "The Shot," a basketball move in which John lifts Owen up for a slam dunk. They perform this maneuver over and over, trying to accomplish it as quickly as possible.

PARGRAPH When the boys are old enough, they enter Gravesend Academy, where Owen thrives: he has a powerful column called "THE VOICE" in the school paper, and easily becomes the class valedictorian. Shortly before graduation, however, he is expelled for helping students make fake IDs out of their draft cards--it is the early 1960s, and the Vietnam War is just beginning. After his expulsion, Owen removes a statue of Mary Magdalene from its place in front of a local Catholic school, amputates its arms and head, and welds it to the stage in the Gravesend Academy auditorium. The school minister, the doubt-plagued Rev. Louis Merrill, asks the boys at morning meeting to pray for Owen Meany, and the unpleasant headmaster who expelled Owen loses his job as a result of the event.

Owen manages to graduate from the public high school, and John and Owen are reunited at the University of New Hampshire, where John majors in English; Owen develops a relationship with John's hypersexual cousin Hester. Owen is only able to pay for school by participating in an ROTC program, and he hopes for a combat assignment in Vietnam after graduation, to John and Hester's dismay. He believes that he is destined to die in Vietnam. However, because he is too short to climb over the obstacle-course wall, Owen is given an administrative assignment in Arizona. There, Owen campaigns actively for reassignment in Vietnam. John, meanwhile, attends graduate school. John does not want to go to Vietnam, and Owen helps to ensure that his friend will not have to go to war by amputating John's right-hand index finger with a diamond saw.

In 1968, Owen begins working as a casualty-assistance officer, escorting the bodies of dead soldiers back to their families. One day, he calls John and asks him to meet for a few days in Phoenix, Arizona, where Owen is on assignment. John flies to Phoenix, and he and Owen spend a few days relaxing; John meets the bereaved family Owen is then helping, which comes from a trashy part of town. John especially notices the dead soldier's younger brother, a hulking, menacing fifteen-year-old named Dick Jarvits, who lives for the day he will be able to travel to Vietnam and slaughter the Vietnamese. When John and Owen go to the airport for John's return flight--on the day that Owen believes he is destined to die--they see a group of nuns escorting a column of Vietnamese war orphans through the halls. One of the nuns asks Owen to take the boys to a men's room; there, Dick Jarvits bursts in with a grenade. He hurls it at John, who tosses it to Owen; Owen leaps into the air, and John holds him up so that he can thrust the grenade into a high window alcove--a move exactly like the The Shot. The children are shielded from the blast, but Owen's arms are blown off, and he bleeds to death.

Back in Gravesend and before Owen's funeral, John goes to see the Rev. Merrill. During the meeting, Owen's ghost possesses the reverend and causes him to admit that he is John's father. The reverend claims that he prayed for John's mother to die just before the foul ball hit her, and that, in vengeance, God has turned his face from him. To restore his father's faith, John plays a prank in which he places a dressmaker's dummy in such a way as to make the reverend think he is seeing John's mother's ghost. His faith restored, the reverend delivers a passionate eulogy for Owen, calling him his "hero" and pleading for God to give him back.

From his house in Toronto, John remembers that also before the funeral, he paid a visit to the Meanys, where Mr. Meany reveals a shocking fact: he claims that Owen was a virgin birth, just like Jesus Christ. He tells John that he told Owen this when Owen was about eleven--about the same time that Owen accidentally killed John's mother. John considers this revelation monstrous, and says that it cannot be true. It remains unclear what John believes about Owen's parentage, however, and the mystery is never explained.

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