The main theme in the story "The Son of Neptune" is that you have to protect what is precious to you. In this case, Percy struggles through many obstacles in order to protect his "family", which in this story, is Hazel and Frank. He also fights to regain his memories and to re unite with his girlfriend Annabeth.
Another possible theme in this story could be family. All throughout the story, Percy treats his friends like his family. In the end of the book in the last few pages, believe he said something like "I want you to meet my other family" referring to his old friends at camp half-blood.