When the Pope was toppled, there was an attempt to assassinate him, but this failed, and it was since decided not to make him a martyr to the few surviving Christians. Since then, Christianity has been eradicated, and the pope is now the last surviving Christian.
In the story, the Pope is flown for a formal meeting with the General, the new leader of the new world order. After many long years, it is a formal meeting, much publicized in the world press. The pope's robes and even his papal ring are restored to him from the World Museum of Myths, and he is forced to don them for the occasion, faintly remembering earlier days when they were his normal attire. At 11:30 am sharp, he is taken to meet the general, who reminds him that he is "The last Pope, but still a Pope," and therefore still a threat. The general places a gun on the table and offers him an opportunity to die with dignity, "The last Christian. This is a moment of history." After many long years of isolation, this is a relief to the Pope. The two men share a glass of wine before the execution is to take place. His last words, before he is shot, are Corpus domini nostri ...
Greene ends the story by reflecting on the General's concern that Christianity may be abandoned and its last believers persecuted, but that somehow the faith will survive. Even after performing the execution himself, the General is plagued by the doubt, "...is it possible that what this man believed may be true?" Even religion's greatest enemies, Greene is saying, still live with the question of what if they are wrong, and as long as the slightest doubt remains, Christianity will survive. Even though he is frustrated by the modern world's skepticism, he believes that that very skepticism may yet be what keeps Christianity alive.