While most coming-of-age novels deal with the protagonist's attempt to discover his own identity, I Am the Cheese adds a twist. Adam's identity is out there somewhere, but it is buried beneath two separate, horrific layers. Not only is he someone else—Paul Delmonte, before the government changed his name in a witness protection program—but he has trouble remembering this fact, as well as most of his experiences that occurred prior his institutionalization. Cormier uses the typical narrative arc of the adolescent protagonist—the teenager discover his identity by the end of the novel. Adam's identity becomes clearer just before the end of the novel. Cormier alters the typical arc, because the truth of Adam's identity is so horrifying that Adam cannot comprehend it. Instead, Adam withdraws into a somewhat infantile state and repeats his imaginary search for his father. Adam discovers his identity, and then rejects it.
Moreover, Adam's father and mother have also had to confront the emotional difficulties of assuming new identities. Anthony Delmonte has to give up journalism and Louise gives up her social world in Blount for a life of fear and distrust. In some ways, changing one's identity is simple: Grey has a number of aliases, including a number. Grey is thus everywhere while also being a nothing, just as Adam describes. Even Adam finds how simple it is to lie to Amy about his past and invent a new "set of circumstances." Amy, on the other hand, may lie at times with her Numbers pranks, but she never lies about herself. Amy is forthright, honest, and does not shy away from her fears and faults, and even talks about her gas noises in the bathroom. The term "identity" is a vague one that can mean so many things—one's race or gender or even one's birthday. One meaning of identity is that it defines the person or thing to which it is attached, and it makes some logical sense, or develops into a meaning. The characteristics of one's anatomy define race and gender, and for his mother, Adam's birthday falling on Valentine's Day symbolizes love. Consider how significant your phone number is for you, even though it is a completely arbitrary set of digits. For the Delmontes, their new identities are the offspring of fear and fear alone, given by Grey without any of their own input, and it is impossible for them to grow into or accept the new definitions by which they must live.
Three different organizations control the helpless Delmontes/Farmers throughout the course of I Am the Cheese: the organization Anthony has testified against, Grey and his department, and Brint and the institution. Anthony is a courageous journalist who stands up for what he believes in, though it means testifying against a powerful organization with possible links to other criminals. Only after he is almost killed several times does he accept that the organization will eventually murder him unless he joins a second organization—Grey's witness protection program. There, the Delmontes are at Grey's whim, forced to live without much freedom. The second organization, a government-sponsored program, is also corrupt. Grey fears that Anthony is withholding important information from him, and Grey uses the program to gain his trust and try to extract the information. Grey eventually kills Anthony and his wife, with the help of the first organization, to which he is evidently connected. Lastly, Brint is an even more sinister force, and he claims he is helping Adam recover his lost memory. Brint, however, only wants to see if Adam knows the secret information. Brint medicates Adam, plays mind games with him, and is self-admittedly cold and stoic. Cormier reveals that Brint works for the same organization as the corrupt Grey, and wants to reinstate Grey into the "Agency" despite evidence that he helped murder the Farmers. All the anonymous organizations are connected in an insidious web, while the individuals are left to fend for themselves in a battle they cannot win.