The Road to Chlifa begins in Montreal, Canada, where seventeen-year-old Lebanese refugee Karim Nakad arrives in his new class. Alternately told from the perspective of an unnamed classmate and Karim's diary, the opening section of the novel establishes how Karim garners unwanted attention from both boys and girls, with the girls fawning over his good looks and the boys being jealous. Dave, a particularly disgruntled student, mutters about Karim being "a bloody Arab."
In his diary, Karim writes of how he despises his new home and writes letters to his friend Béchir detailing everything he hates about the country. While Karim is simply sullen and withdrawn most of the time, he occasionally experiences outbursts of emotion, often unintentionally triggered by an Asian immigrant classmate named My-Lan. Karim's classmate's narration describes how Karim's presence works as a catalyst that disrupts the delicate balance of the class. Part I culminates in a school ski trip. While drinking in the boys' bathroom, Dave and his gang sexually harass My-Lan. Karim hears her cries and intervenes, taking his rage out on Dave by pummeling him. In the fight, Dave injures Karim with a knife, and Karim is evacuated to a hospital.
Part II moves back in time to the previous summer, when Karim was still in Beirut, Lebanon. Just before fighting ramps up in the last year of the Lebanese Civil War, Karim's family visits his grandmother in Montreal, leaving him alone to study for his baccalaureate exams. As the violence in the city worsens, school is canceled, and Karim spends his time with his friend Béchir and his crush Nada. Eventually, Béchir's family flees to Paris out of concern for their safety. Karim stays because he is in love with Nada. However, one day Karim goes by Nada's house only to discover that a bomb has destroyed her building and killed her. Her little sister, Maha, and their baby brother, Jad, are the only survivors of the Tabbara family.
While processing Nada's death, Karim accompanies Maha and Jad on their journey to Chlifa, a city beyond the Mount Lebanon mountain range. Maha says friends of her parents live there and will take care of them. To cross the Green Line buffer zone that separates Christian East Beruit from Muslim West Beirut, Karim pretends his father's journalist friend Antoine Milad is his and Maha's uncle. Antoine helps the children with the journey by giving them maps and camping supplies to get through the mountains.
On the long trek to Chlifa, Karim and Maha oscillate between feelings of mutual hostility and respect. Along the way Maha finds a goat named Black Beard, who travels with them until Black Beard gets blows up after stepping on a landmine. The event triggers Maha's trauma of having lost her family: she admits she was always jealous of her sister's beauty and her breasts. She feels guilty for having lived while her perfect sister died. Karim consoles her and they fall asleep: he wakes up to realize he is groping Maha's tiny, child's breasts. When he pulls away, Maha is insulted and asks if he would prefer to touch Nada's body. Karim insults Maha and then takes a walk to collect himself. When he returns, though, he finds Maha's half-naked body behind a rock: blood trickles from her crotch and streams out of a slit in her throat. Karim carries her to Chlifa, buries her, and brings Jad with him to join his family in Montreal.
In Part III, the narrative returns to Karim in the hospital, where he reveals that My-Lan reminded him of Maha, and that was why he was hostile but protective of her. People now joke that My-Lan is Karim's girlfriend: he says that isn't the case, but he looks forward to seeing her every day. The book ends with Karim sending Béchir a letter detailing the reasons he likes Montreal. Karim suggests that he may become a doctor and return to Lebanon to help rebuild the country.
