As such, it is basically Apocalypse Now (or Heart of Darkness if you prefer) for Christians, and has much of the same discourses evident.
First, there are the graphic images of violence, much like those in the Vietnam or African scenes of the oeuvres above. People are crucified, showered with boiling water, drowned, beheaded, and hung upside down in pits to bleed dry. In the religious context of the film, it constitutes the Christian torture porn of Mel Gibson's Passion of the Christ and thousands of years of Christian imagery. The cathartic violence of Christian imagery has served as both titillation and a badge of shared identity since its inception. This visceral violence fits perfectly with the Japanese antagonists, samurai who are as sadistic as the depictions of bushido in Nanjo Norio's classic novel Shigurui (Crazy for Death). Indeed, viewers of Silence are treated to fervent foreign priests, pious Japanese peasants, and two-faced samurai who are all equally 'crazy for death.' The largely male nature of the cast also adds a masochistic homoerotic tinge, equal parts Yukio Mishima disembowelling himself and the twelve disciples washing and kissing each other's feet. The inquisitor Inoue and his lackeys top this off with their simpering, overacted sadism, which validates Nanjo's assertion that bushido was only possible in a society constructed of a mass of masochists at bottom and a few sadists at top.
Next, Japan and the Japanese themselves constitute the jungle of civilized savages that has made up much of their depiction by westerners. Besides being all 'crazy for death', they are depicted as inscrutable when Garfield's priest describes their faces as 'masks', a common trope Ian Littlewood (1994) has explored deeply. They are also portrayed as inhuman, unfeeling of fear of death, or pain, unlike the priests who agonize over these threats. This is a clear discourse of western cultural superiority, a humanity the Japanese lack because of their misunderstanding of the religion that supposedly is the fertile soil of its growth. Indeed, the inquisitor Inoue calls Japan a 'swamp' in which the seed of Christianity rots, again echoing the jungle image of Apocalypse Now or Heart of Darkness. As such, the film recreates the battle of the conflicting discourses of bushido's physical hegemony and Christianity's spiritual hegemony. Although these are depicted by the inquisitor Inoue as a clash of civilizations or cultures, in truth they are also a naked power play for the body as well as the soul of Japan by means of dominating the bodies and souls of Christians there. Inoue's offer of life to those who renounce Christ by stepping on his image is thus a reverse Pascal's Wager, asking why not say you don't believe if their is no punishment, rather the end of suffering?
I haven't read Endo Shusaku's original novel, but I have read his novel Samurai, which is almost the inverse tale of samurais traveling to South America and finding faith in Christianity there. Samurai was a nuanced work, with Christianity serving as the only option in a world of dominance and suffering by the enforced karma of Japan's vertical feudal society. Silence has much of the same themes, but by putting westerners at the centre it robs Japanese of agency, and thus both their sadism and piety are rendered meaningless. The final shot of the film, which shows the final, inner victory of Christianity, also seems hollow as this victory was only possible by the white male's painless sacrifice of apostasy and becoming a member of the Japanese hierarchy, and not the sacrifices of the many Japanese who gave their lives for a foreign god.
Littlewood, Ian (1994) The Image of Japan. London: Seeker & Warburg.
Nanjo, Norio. (2012). Shigurui 1. Tokyo: Akita Bunko.