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.
Brint is a cold, calculating figure. His only desire is to see if Adam knows anything about the information his father testified about. Brint manipulates Adam during their conversations, and makes him believe that he is merely a "guide." Underneath his cold stoicism there is something sinister about the way Brint evades questions and sedates Adam, but the worst revelation comes at the end, when we find out that Brint works for the same "Agency" as Grey and, despite knowing that Grey has betrayed the Farmers, seeks to reinstate Grey and "terminate" Adam. As such, Brint is a looming example of corrupt authority. Though he could have been a father figure to Adam, who is in desperate need of one, he victimizes Adam in the same way Grey and the family's "Adversaries" did to the Farmers. One of the more harrowing details of his relationship with Adam is Adam's acknowledged dependence on Brint. He knows Brint is using him for some reason, but needs him to restore his memory.
Anthony was an upright journalist who bravely investigated the corrupt government. After his reluctant identity change, Anthony became David and lived in fear of being found out. David takes the job of an insurance agent, which is particularly ironic: David's duty is to provide protection for people in the event of an accident, while the government provides protection to David. David handles the relocation better than Louise, and he stoically accepts Grey's orders for his new life, while holding out hope that he will return to journalism. Every so often his façade cracks and he exposes his sadness. The one positive effect of Adam's discovery of the truth is that David and his son grow closer. However, David makes sure to withhold certain information from his testimony from Adam in case he is ever questioned.
Grey, also known as Thompson or #2222, is as mysterious a figure as his multiple names indicate. He protects the Farmers and is quite good at his job, helping to foil the two murder attempts. All along, Grey hides his real intent—to make sure David has revealed all possible information from his testimony. His personal stake in the matter suggests that the information could possibly harm him, although this is never explicitly stated. Grey becomes a fixture in the Farmers' lives, but his presence is somehow invisible too. Grey's status as a cipher—or a "nothing," as Adam calls him—is what he eventually turns the Farmers into, as well: humans who have little residue of their own identities.
Louise has the hardest time adjusting to her new life. She sequesters herself in her room and is unable to maintain intimacy with Adam and David. Moreover, she lives in fear of what she calls the "Never Knows"—never knowing what will happen next, never knowing whom to trust, never knowing if the next phone call is from an enemy. More than the rest of the family, Louise grasps most to her past, making weekly calls to her only living relative, Martha, a cloistered nun. She is also the only one who defies Grey, saving some mementos from their former life despite the risk, and openly admits to Adam her hatred of him. Louise despises how a man whose very name is a mystery can puppeteer their lives.