Identity
One of the central themes of the novel centers around Zits’s changing identity. Initially, Zits feels he has a skewed identity - he is an outsider, with no fixed race and no home. As such, he defines people by their wealth and their beauty. His magical journey helps him realize that he is in control of his own identity, by giving him insight into several other perspectives. Hank is an insider, the Indian boy has a community, Gus has power and talent, Jimmy feels out of control, and his father nurses similar resentments to his own. Each of these identities speaks somewhat to Zits's confusion, and yet he realizes that every person has inner conflicts and moments of confusion. Ultimately, what Zits realizes is that one's identity is defined more by his behavior than by his race or wealth. There is no magical identity that solves all problems. Instead, each human must battle himself to be someone he is proud of.
Family
The greatest absence in Zits’s life comes from his lack of family. His foster parents, group homes, and his peers offer little substitution for a real family, and his most extreme pain comes from his father's abandonment. His early life is a series of betrayals, by his father, by his mother's death, and then by his Aunt Zooey. However, his transformations make him realize that no family is perfect. He sees varieties of family situations through his different identities, and realizes how every human is capable of betrayal. Hank Storm’s family loves him, but does not know that he is a killer. Jimmy cheats on his wife. Gus leads the soldiers to the Indian camp where families are literally torn from one another. Zits’s father is alone, tortured by the choices he has made. The big exception is the Indian boy’s family, which makes Zits feel he is in Heaven. However, even this situation is tempered by the violence they commit. Even though the novel ends with the prospect of a happy family situation with Robert and Mary, there is no magical solution to family problems. Instead, the human penchant for cruelty and violence means that we have an unfortunate tendency to hurt those whom we ought to love the most.
Betrayal
The concept of betrayal is portrayed in many forms throughout the novel. Zits betrayed societal norms by opening fire in the bank, on people who trusted him to respect their lives. Jimmy was similarly betrayed by Abbad. Elk and Horse commit a different, more political kind of betrayal through their treason against their own people. The examples are plentiful, and all together suggest that humans have a tendency to hurt one another. As a result, a cycle of cruelty is perpetuated, as happens with Zits, who responds to the betrayals of foster families who abuse and neglect him by turning to violent hatred. Throughout the novel, Zits learns not only that betrayal is a natural human vice, but also that one must accept this weakness in order to forgive and find serenity. When he finally empathizes with and then forgives his father - he who betrayed Zits first in life - Zits is finally ready to mature.
Shame
Zits is overwhelmed with shame, and much of his journey lies in overcoming that shame. He is most immediately shamed by his appearance, dominated so much by his acne that he names himself for it. However, he makes little effort to change his appearance because he does not feel worthy. He is more deeply shamed, over the pain of his father's betrayal and of the sexual abuse that made him feel unlovable. However, the shame is not what causes Zits's problem; instead, it is his self-imposed defenses, which he put up in response to that shame. Ultimately, what Zits learns is that he must accept his shame as a part of himself - realizing that every human battles different degrees of shame - so that he can open himself to the possibility of hope.
Violence
The novel is infused with violence at almost every point. In response to the emotional violence of his father's betrayal and the physical violence of sexual molestation, Zits has developed an affinity for violence and fighting. He has learned to close his emotions off, and to respond with aggression to any challenging situation. Unfortunately, this attitude enables a cycle of violence, which Zits does not know how to break. This manifests in the atrocity he commits in the bank.
His many transformations reveal how innate violence is in all human history. Every transformation is full of murder, cruelty, and torture. By seeing these atrocities from a detached perspective (inside other human beings), Zits confronts the truth of violence, its ugliness. This new insight leads him to eschew such a response to his life's challenges. Learning from his experiences in time, Zits thankfully begins to turn away from violence at the end of the novel.
Hate/Revenge
Hate and revenge motivate many of the decisions made by Zits and other characters in the novel. Hate acts as a precursor to revenge - one does not exist without the other. Zits hates the elite of his country, he hates the foster system, he hates the men who have abused him, and he hates his father who abandoned him. Justice's lesson to Zits is to activate that hatred into vengeance.
Because of what Justice teaches, Zits feels justified in committing such an atrocity. However, his transformations reveal to him how any human can rationalize atrocity by focusing solely on his own hatred. Gus feels justified in massacring Indians in the same way that the Indians felt justified in desecrating the bodies of Custer and his men. By seeing that different perspectives and justifications do not mitigate the ugliness of violence, Zits realizes that the greatest ugliness is the human ability to hate without feeling guilty. Once he can see his own atrocity at the bank in these terms, he repents and is given a second chance. We are left to believe he will endeavor to conquer his own hatred as his life progresses.
Forgiveness
Before the incident in the bank, Zits is unapologetic about his behavior. His actions are aggressive and forceful. He has little hope for himself; his future seems dim. He has neither the desire for nor the expectation of forgiveness.
However, what he learns through his transformations is that he must first truly accept himself as flawed if he is to forgive. Having constructed such an emotional shield, Zits barely feels obligated to consider the sources of his shame. In all of the different bodies he inhabits, he realizes how in focusing on one's own shame and hatred, one is driven to unhappiness. As he learns that every human is capable of betrayal, he begins to empathize with people like his father, and then is he able to forgive them. Once he begins to forgive others, he is able to confront the truth of his sexual molestation, and then find the strength to forgive himself, to seek a better life. The final chapters suggest that Zits has found redemption not because he has found a way to live without hatred and resentment, but because he has learned that he can forgive himself, that he does not need to solely define himself by his vices.