The over-reaching conflict that the entire series is concerned with is the battle between good and evil.  The protagonists in the real world are fighting a mythical battle against evil forces, forces that represent the dark side of human nature.

In this particular book, there are individual and concrete conflicts with each character.  Will has to struggle with his need to remember information lost to his illness, as well as with the need to be isolated to recover.  Bran has to struggle against alienation from society based on his disability, his confusion and pain at discovering his true identity, and his strained relationship with his stepfather.  Both boys struggle also against the antagonism of Caradog Pritchard and his irrational behaviors.