The Irrelevance of Theology
Rycker can safely be called the human villain of the novel. The thematic villain of the book, however - and the means by which Rycker is represented as villainous - is theology. Blind, rigid, pure adherence to Catholic dogma characterizes both Father Thomas and Rycker. Much like the Pharisees in the New Testament, these characters display their religiosity with pomp and ostentation. This holier-than-thou attitude depends largely upon their ability to argue arcane points of moral theology - a subject that, Greene suggests, has little relevance to the lives and suffering of actual people.
One moment in the book symbolically captures this theme. In the last scene, Doctor Colin diagnoses a young child with leprosy. The Superior remarks that the child had previously come to him for sweets. In a flash, Greene captures the futility of dogma versus the value of medicine. The Superiors "sweets" - his theological bon-bons, his saccharine sermons - could not save the child from leprosy. Doctor Colin's scientific methods, on the other hand, can.
Similarly, Querry - a man who professes nothing but disdain of theology - acts more Christian than any other person in the novel. Greene, thus, upholds the value of Christian behavior (that is, selflessness, generosity, sacrifice) while showing that there is no essential link between mouthing dogmas and being Christian. Indeed, those who mouth dogmas are inevitably the saps and villains in Greene's bleak world.
Suffering Versus Discomfort
Querry's first words of the novel - "I feel discomfort, therefore I am alive" (9) - have been transformed in his memory by the novel's end to "I suffer, therefore I am" (186). This transition from discomfort to suffering is nothing less than the movement from being a "burnt-out case" to being cured, to finding meaning in life.
As Doctor Colin remarks, the leprosy patients who despair and lose their will to exist are not those in the throes of suffering, but those who have been ostensibly cured. Their mutilations no longer hurt - they are merely uncomfortable. Suffering is a sign of existence; the suffering patient does not consider the misery of his or her condition. The patient whose stumps are numb, on the other hand, is in a more existentially compromised position. Querry, like Deo Gratias, is numb to life. He cares for nothing, therefore he doesn't suffer. He has nothing to lose. He merely feels discomfort.
By the novel's end, though, Querry has something to lose again. Paradoxically, he has gained something to lose, and therefore he is a whole man. He is free to suffer.
The Importance (and Unimportance) of Being Famous
Querry's fame, at least at this point in his life, is very unimportant to him. Indeed, it's his greatest burden: the reason he wanted to run away from Europe, and the reason he runs into trouble in Africa. It is much more important to others, especially to Rycker, Father Thomas and Parkinson. The reason for this is rather simple - these unimportant (yet self-important) men see in Querry an opportunity to increase their standing in the world. If they can rub shoulders with the Querry (as Rycker incessantly dubs him), they must be big news themselves, right?
Rycker justifies his use of Querry's fame by repeatedly insisting that the famous belong not to themselves, but to the world. Unfortunately for Querry, this seems to be true. He cannot remake his life, no matter how far he runs. Some nosy soul will claim his attention, force company upon him, interpret his actions and beliefs for him - in short, live through him. Querry's actual words and beliefs have nothing to do with the way he is represented. The famous man, it seems, is little more than a convenient canvas for others.
As a side-note, Greene first got his idea for A Burnt-Out Case through personal experience. After writing several searching "Catholic novels" (though he always loathed that term himself), Greene gained an undeserved reputation for piety. The faithful Querrys and Father Thomases of the world pestered him for his religious opinions. A Burnt-Out Case, then, can be seen both as a manifestation of this experience and as a purposeful stab at his tormentors. In depicting Querry - the atheistic Catholic - he may be attempting to shed his title of "Catholic novelist."
Leprosy as Metaphor
Both Doctor Colin and Querry regularly refer to psychological conditions as equivalent to leprosy cases. This metaphorical equivalence can be both very specific (as in the exchange on p. 46, where Querry talks about himself as "one of the mutilated") and rather general.
The specific metaphor goes more or less as follows: Querry considers himself like a "burnt-out case," a leprosy patient who has ceased his physical suffering but who has been mutilated beyond self-recognition by the disease. Just so, he has ceased feeling his crises of faith, vocation, love, etc. He is no longer interested in such once-tormenting questions; he is merely a mutilated man, uncomfortable, aimless and bored. In the course of the book, he recovers his feelings. He learns how to live with his "mutilations," like other burnt-out cases (Deo Gratias, for instance) learn how to complete life's simple tasks without fingers and toes.
More generally, leprosy provides Greene with a means to physically symbolize psychological conditions. We are all, to some degree, lepers, suffering through life. Some are cured, some succumb to the worst of the disease. We heal ourselves with faith, with good acts, with the praise of others, with sex. Life is, in a way, a disease: we either learn to survive it, or we don't.
Vocation and Sex
Greene suggests a parallel between one's sex life and one's working life: that when one is productive in one, one is active in the other, and vice versa. This doesn't hold true for everyone, of course - Doctor Colin remains committed to his calling, though he is celibate, as do the priests. It's specifically true of Querry.
In discussing his disillusionment, Querry repeatedly observes that as he lost interest in his work, he simultaneously lost interest in his sex life. Indeed, the two are closely related in his backstory. His philandering leads to the suicide of a mistress - Marie - around the same time that he loses faith in his calling as an architect.
Thematically, the two categories have something in common. Both sex and architecture can lead to a procreation of sorts. Querry's fame as an architect "immortalizes" him, to a degree, just as sex can lead to the propagation of one's genes. Of course, Querry has no interest in children, but the sexual act is still associated with vital power - here and in the future. As he loses interest in life, he loses interest in the future. His creative acts, in both the figurative (architecture) and literal (sex) senses of the term, become meaningless for him.
Absurdity and Theatricality
At several points in A Burnt-Out Case, Greene makes sure to emphasize the absurdity of his tale. This absurdity is linked consistently with theater, which makes sense - theater can be seen as a hollow version of life. Just so, Querry has arrived at an awareness of the hollow theatricality of existence. He has been proclaimed famous, lauded internationally, hounded by the press - all of which seems absurd to him, as his own existence is utterly without value in his eyes.
The theatrical strand in the novel comes to a head in the final Part, in which Rycker plays a farcical "cuckolded husband," a stock character in French comedy of the time. Rycker melodramatically goes through his part, brandishing his gun and declaring his righteousness. The whole scene comes off as ridiculous, given that he hasn't even been truly injured. Nevertheless, his absurd lengths come to a tragic head - he plays the role right up to the killing of his supposed rival, Querry, who thus dies under completely absurd and pointless circumstances.
Absurdity is a consistent theme in what might be termed "existential" literature. Without God, the affairs and dramatics of the human condition seems hollow and meaningless; existential philosophers often speak of recognizing and embracing life's absurdity. Querry perhaps takes their advice, acknowledging the pettiness of life even as he attempts to create a space for meaning.
Fittingly, Querry's last words are, "[T]his is absurd or else..." We never hear the other option - which is not to say that there isn't one, just that it's obscure and indescribable, at least within the world of anxiety and black comedy that Greene gives us.
Pendélé
While Deo Gratias remains more or less a mystery throughout the book, he does serve to introduce a major thematic term - Pendélé. This term identifies a place Deo Gratias once went with his mother - a waterfall - where he says that they were happy. It represents everything he has lost in the course of his leprosy. When he wanders off into the woods and gets stuck in the bog, unable to help himself out, he goes in search of Pendélé.
Querry takes up the term to represent the lost happiness of childhood that most people feel. Pendélé is a place of innocence - a psychological more than a physical location. One can perhaps never go back to it, but its existence is nonetheless important. Pendélé creates hope amidst suffering; it is, more or less, a substitute for heaven. Querry (and Greene) doesn't endorse the idea that there is a heaven, but the ideal past seems close.