The wise reader will read this book and feel the mastery of Greene's story-telling as moment by moment, Bendrix's disposition betrays him more and more. His writerly instincts lend themselves to calculation of human motivation, so every time he encounters someone, he is reading not only the surface level, but also the emotional subtext. Over time, Graham Greene shows that this is a hubris, the tragic downfall of which is severe paranoia and distrust.
Bendrix is on a journey, but it is different than the one he thinks he is on. His journey seems on its surface like a quest into love, or at least a navigation of romance, but the truth of this story shows that just past The End of the Affair, there lies another domain of emotion and knowledge. His affair with Sarah has him so invested in his personality performance that he forgets the sublime. Then, when she dies, he realizes that he was never up against a competitor (he thinks he is competing for Sarah's love with another man). He was up against fate and the horror of human death.
Truly, the antagonist in Bendrix's story is not Sarah or Henry, as he sometimes feels, oscillating between hating one, hating the other, hating both, and hating neither. The true antagonist it seems is Graham Greene himself. The religious subtext of the novel is quite clear. From the Catholic characters and their constant reflections on God, to the burial rites denied to Sarah, the tone is stern and religious, but the ultimate effect is that Bendrix sees the hand of God in his fateful tragedy, and his angery toward God is the final note of the novel. He tells God to just leave him alone. The "god" in question might more properly be the story-teller who let Bendrix suffer thusly. The wise reader will shutter in the dual agony of pity and fear.