The "overall message" of any novel could also be considered its theme and most novels of length have more than one theme. One of the most prominent themes of this book is the idea of prejudice and how war stimulates immediate bias and hatred between two groups of people. In this case, it is the Americans versus the Japanese and, more specifically, Japanese living in America. Historically, this theme is not specific to the novel alone but is a realistic reminder of authentic attitudes and authentic events in America's past.
Another message of this book is the idea of interracial love during a time in history when it would have been considered socially inappropriate on several levels. The crumbling of Ishmael and Hatsue's young romance and the future feelings of bitterness and confusion are both evidence of societal influence that was far more negative in our culture during WWII than it is today.
Arguably, it could be said that the author's main purpose and overall message in writing this novel was to show real human needs, emotions, and reactions to circumstances very much beyond their control. Setting his novel around the difficulties of the Japanese Americans during and after WWII was his lens for heightening the legal, romantic, and historical tones of their needs, emotions, and reactions.