Motherless Brooklyn traces Lionel's growth from an orphaned child, to one of the Minna men, to an independent sleuth, to a legitimate car-service employee. The novel is in many ways a classic bildungsroman—a novel that deals with the formative years of an individual, that tells of the search for identity, truth, and sexual maturity. One of the central themes of the novel is Lionel's quest to discover his own identity, to find his place in the world as a real detective. Lionel's countless tics on his name are one way the novel represents this search; Liable Guesscog, Laughing Gassrog, Confessdog, Freakshow, Valiant Daffodil, Alibi Diffident, Final Escrow, Ironic Pissclaim are all, although apparently random verbal tics, representations of parts of Lionel's personality. Lionel's quest for Frank's killer also becomes Lionel's quest for his own identity. It is only through Frank's death that Lionel can become his own person; only through becoming Minna's avenger can Lionel become himself, a true detective at last. Lionel says at the beginning of the novel that "the distance between me and me was enormous"; through solving of the mystery of Frank's murder and through narrating the story, however, Lionel closes this gap. An important aspect of Lionel's self-discovery is his attempt to establish connections with others, symbolized at first by his possession of other people's cell phones and beepers. The novel moves from Lionel randomly answering other people's calls and messages to successfully establishing his own social relations, first with Kimmery and finally with Julia and the other Minna men.

The compulsion to play with language or the outbursts of Tourette's are clearly linked to Lionel's emotional states. One can see this in Minna's death scene, for example, which is punctuated by a sequence of jokes which themselves grow increasingly more punctuated by Lionel's Tourette's as he gets more upset. "Guy walks into the ambulance ramp stabs you in the goddamn emergency gut says I need an immediate stab in the garbage in the goddamn walk-in ambulance says just a minute looks in the back says I think I've got a stab in the goddamn walk-in immediate ambuloaf ambulamp octoloaf oafulope." In other words, Lionel's language expresses emotions in ways which "standard" language cannot. The punch line of the joke "I'm a frayed knot . . . I'm afrayed . . . we don't serve string" links joking—Lionel's way of communicating with Frank—to Lionel's feelings. Tourette's here becomes a way of expressing emotions that would be left unsaid otherwise, a way of connecting with other people.

Indeed, almost all of the major characters are involved in similar quests: Lionel, Julia, Gerard, and Kimmery are all searching for their own identities and their place in society. None of the major characters are who they appear to be: the Minna men are not really a car service, Julia is not really a tough-talking dame, Gerard is not a Roshi, and the Buddhists are a front for a money laundering operation. In fact, the Minna men are not really a detective agency either; they perform odd jobs for Frank Minna, but they do not know what they are doing or whom they are doing them for. In other words, even if the front of the car service is removed, there is another layer of deception underneath. Thus, the novel is both a mystery in which characters are not what they seem, and a quest story in which characters are seeking to discover who they really are. In the process of discovering who others really are (Gerard, Julia, the giant), Lionel discovers who he really is. The fact that Lionel does not discover his "true" identity in the sense of his true parents does not mean that he has not discovered a truth; indeed, what he discovers is that truth is layered, consists of layers of stories, of what Frank calls "wheels within wheels." In other words, the truth is a series of deceptions or stories, just as Lionel's "true" name is the series of variations his Tourette's produces. What Lionel discovers is that all identities are inventions of sorts; in the end, however, Lionel moves away from Frank's...