Adam is alienated from everyone around him. Unlike most adolescent protagonists who are uncertain about their identity and feel isolated from others, there is a concrete reason for his paranoid behavior. While in the psychiatric hospital, Adam is put on heavy medication in the hope that he will divulge secrets that his father had withheld from the government. He is not fully conscious of his identity and his past because the medication—and the trauma of losing his parents—have altered his memory and sense of reality. Unlike many adolescent protagonists, Adam is not angry at the world's injustices and he is not overly confused with his sexuality or just going through puberty. Rather, Adam's identity problem stems from his inability to understand his identity, because it has been physically and psychologically taken away from him. Adam—or Paul's—identity was changed when the Delmontes joined the witness protection program. Next, due to the psychological drugs and the chaos of losing his parents, Adam cannot regain his memories and does not remember his past.

Even before his father confesses to Adam about their Farmers' identity change, Adam senses there is something wrong with his family. He feels that something has been different since their bus trip to Monument, and as a result, he lives in fear. Adam's worries originate, and persist, as a fear of dogs and closed spaces. His fears develop into concerns over whom to trust. He is horrified to discover the truth behind his lost identity. But Adam is resilient too. He ploughs along on his bike trip to Rutterburg, braving the elements and enemies, and he even plays a competent detective when learning about his family's secret.

Adam's relationship with his parents, before the truth is out, is mostly stifled. After the revelation of his family's past, Adam grows closer to them. He finally understands the origins of his fears, and he bonds with them over an uncertain past and future. The song they often sing together—"The Farmer in the Dell"—resonates the theme of a unified family, not a forced ritual. Adam's father originally intended to use the song to make Adam believe that his family's name was Farmer. Adam's emotional world largely comes out in his interactions with his girlfriend, Amy. She brings him out of his shell, and she is the one person with whom he is not afraid to share his dreams of becoming a writer. Adam, however, feels guilty and sad that he can never tell her about his family's past. Adam's interactions with Brint are completely different—Brint forces Adam to open up, often against his will, and divulge secrets Brint wants for his own purposes. By the end of I Am the Cheese, Adam finds out he is doubly orphaned: not only are his parents dead, but so is his own identity. Adam's search for the truth, which is buried beneath his spotty memory, is horrifying. We learn at the end, this will only be repeated again in a cycle until he "obliterates." He understands that he is like the cheese in the "Farmer in the Dell," and utterly alone.