The theme of a novel is implied. This means it is not usually directly stated in a short story or a novel.
You read the book and you realize something. It is "the author's message" to you. You can watch and see how the main character learns something and changes. If you look closely, at how the main character changes you will often see the "theme" of a novel emerge.
The plot of a novel refers to the action of the novel. It is "who does what to whom". It is what happens in a story. it is very different from the author's message or the theme.
The theme is much more about "why" a character is transformed or changed.