Flight begins with Zits waking up in a new foster home. Not liking his new family, he shoves his foster mom against the wall and runs out the door. Eventually Officer Dave catches up with him and takes him to jail. While in jail Zits meets Justice, a young white boy who takes Zits under his wing. When Zits is released from jail he finds Justice and they begin their training on how to shoot people. Once Justice believes Zits is ready to commit a real crime, he sends him off to a bank. After opening fire in the lobby, Zits perceives he has been shot in the head, ultimately sending him back in time.
During his flashback, Zits transforms into many different historical characters. The first character he transforms into is FBI Agent Hank Storm. While in Hank's body Zits witnesses a meeting with two Indians involved with IRON. He watches his partner kill an innocent Indian and is forced to shoot the corpse in the chest.
The next character he becomes is a mute Indian boy. He is thrown back into the time of General Custer's last stand. He gets to witness this historical battle and at the end is told by his father to slash a fallen soldier's throat as revenge for his own muteness.
While trying to figure out what to do, Zits is taken into yet another character, Gus. Gus is known as "Indian Tracker" and has to lead the cavalry to an Indian camp. Gus is trained to hunt and track down Indians. Trying to take over Gus's actions, Zits forces himself to not attack the Indians. He helps Bow Boy and Small Saint escape from the advancing cavalry.
Next, Zits becomes Jimmy, a pilot who teaches Abbad to fly a plane. He witnesses Jimmy's affair on his wife, and Abbad using the knowledge to carry out a terrorist attack, and Jimmy's suicide.
Finally, Zits ends up as his own father. While in his father's body, he begins to understand why his father left his mother. He also begins to understand that his father does love him and that by leaving he was doing the best for his son.
When Zits reinhabits his own body, he is standing in the bank staring at a small boy. Realizing that his crime could affect many more than just him, he walks out and takes himself to Officer Dave. Knowing he has to help this boy, Officer Dave brings Zits to his brother's house where Zits is offered to stay with them. Zits finally realizes that he can trust these people and for once in his life finally feels at home.