Sherman Alexie's Flight is narrated by its protagonist, Zits, a 15-year-old half-Native American orphan with a history of abuse and an instinct towards violence. After he is persuaded to open fire in a crowded bank, Zits is transported back in time to several different periods of American violence. In each transformation, he embodies a figure in one of these scenes, each of which leads him to reflect on his past and to confront his feelings of angst, loneliness, anger, grief, and identity.
Flight opens when Zits wakes up in a new foster home, his twenty-first. The year is 2007. The author introduces Zits as a half-Native American, half-Irish teen with self-esteem issues and a history of past delinquencies. His most severe disappointment derives from his Indian father's abandonment, which happened when he was born.
After a confrontation with his new family, Zits is arrested by Officer Dave, a compassionate yet rigid police officer. In the juvenile holding cell, Zits meets Justice, a self-named teenage philosopher, and the two boys strike up a friendship. Justice teaches Zits how to shoot guns, and convinces Zits to open fire in the lobby of a bank. Armed with a paint gun and a pistol, Zits kills a number of people before he is shot in the head.
Zits wakes to find himself mysteriously transported back in time to the 1970s. There, he inhabits the body of Hank Storm, an FBI agent who works to counter the Native American civil rights group IRON. As Hank, Zits witnesses the murder of a young Native American man by his FBI partner, Art. Zits is pressured into shooting the young man's corpse, and thereby confronted with the guilt of his own crime at the bank.
Zits’s next transformation leads him into the body of a young Indian boy at the Battle of Little Bighorn, in 1876. The boy had been rendered speechless by a previous bayonet injury. Zits is overwhelmed by the historical significance of the moment, and overjoyed to find that the boy has an Indian father whom Zits can love. However, he is also appalled by the brutality of the battle and its aftermath. When his father tells him to kill a white solider, Zits reflects on the inherent brutality of revenge, and chooses not to strike. To the reader, Zits alludes to his past experiences in the foster system, and the sexual abuse he endured at the hands of one of his foster fathers.
For his third transformation, Zits inhabits the body of Gus, a 19th century Indian tracker with the U.S. Calvary. Gus leads an attack on a camp of Indians, but Zits forces the body to help save a young boy whom he names Bow Boy. He is overcome with admiration for a solider (whom he calls Small Saint) who also helps the boy from duty. Gus’s elderly body suffers from the escape, and Zits eventually sends Small Saint onwards as he waits to fire on the approaching Calvary.
Zits’ forth transformation finds him as Jimmy, an adulterous pilot who mourns the loss of his best friend, Abbad. Jimmy taught Abbad how to fly, and Abbad proved to be a terrorist, killing many people by flying a plane into downtown Chicago. It is assumed that this transformation occurs after 09/11. Zits has less control over Jimmy’s body than he had in previous transformations, and so simply watches as Jimmy’s wife Linda finds him with his mistress. After Linda kicks him out of the house, Jimmy commits suicide by crashing his plane into ocean. Right before the crash, Zits thinks of his mother and father, wishing he could see them before he dies.
Zits’s final transformation is into the body of his father, a homeless Indian man near Seattle in 2007. He initially only knows that the man is a mean alcoholic who refuses the help of two white tourists. When he realizes that the body is his father's, he accesses the man's memories to realize that his father too suffered from a lifetime of pain and disappointment.
After his revelation about his father’s past, Zits finds himself back in his own body, in the lobby of the bank before he opened fire. Reflecting on the lessons he has learned, he leaves the bank and turns himself in. After months of counseling, Officer Dave finds Zits a new foster home with his brother Robert and sister-in-law Mary. Zits is reluctant to trust his new foster family, but they soon win him over, and his hope for the future is restored. The novel ends with the suggestion of a new beginning when Zits reveals to Mary that his real name is Michael.