Challenger Deep follows Caden through the beginnings of his struggle with mental illness all the way until his eventual release from the institution where he was placed for him to get better. We follow Caden's struggle within himself in dealing with his mental illness as well as his trouble accepting the world for what it is.
The book starts with Caden's ordinary life, but it is soon clear that something is amiss when the story shifts to the world inside of Caden's mind where he sees himself of a pirate ship headed to challenger deep. This world in Caden's mind, while confusing at first, allows for a better understanding of how Caden sees the outside world and how he perceives the characters and events surrounding him.
Once his mental illness is discovered by his parents through Caden's odd actions he is placed in an institution to help him get better, where he meets the supporting characters of the book. These characters have their own impact on Caden both in the real world and his fantasy world, where he sees each of their characteristics as useful to the voyage to Challenger Deep. This allows Caden to form personal connections to these characters which helps him see the world around him for what it truly is, rather than living completely entranced in the world of his voyage. These people slowly begin to motivate Caden to want to get better and through confronting reality, he manages to make peace with himself.