Loyalty is a central theme of A Separate Peace. The notion of loyalty is present through much of the novel, but as the novel moves forward the simple loyalty attributed to Finny is complicated and developed into a complex notion relating to individual identity, innocence (and the loss of innocence), and the meaning of integrity.
Initially, loyalty is introduced as one of Finny's most telling characteristics. He is loyal to his friends and to his school in a way that is at once unshakable and innocent. His loyalty is questioned by Gene when Gene begins to suspect that Finny has been competing with him all along. Finny's loyalty is shown to be misplaced when Gene knocks him out of the tree, maiming him.
Gene attempts to reconstruct the loyalty shared between him and Phineas, but the episode in the tree remains between them. This is the beginning of a series of complications that undermine the simplicity of loyalty presented at the novel's opening.
More examples of these complications can be seen in Leper's "escape" from the army, Leper's rejection of Gene and rejection by Gene, Gene's reticence to enlist, Brinker's decision to join the Coast Guard instead of another branch of the service, Brinker's relationship with his father, and Gene's ultimate insistence on identifying with Finny even after Finny's death.
The characters in the novel are challenged to first discover who they are as individuals and then to be true to that discovery. This dynamic feeds into the complexity of the theme of loyalty.