Martin Scorsese stays very close to Shusaku Endo’s novel in his film Silence, so I will treat them as one.
Job is the oldest book of the Hebrew Bible. I understand it as a philosophical dialogue about surely the most stubborn of all faith-related questions: where is God when people suffer? For people with and without faith everywhere and for all time, this thought is a persistent companion. The “silence” of the title is the silence of God in the midst of suffering, in this particular case, the suffering of brutally persecuted Christians in 17th century Japan. From Job to poor Japanese fishermen to the people of Aleppo: suffering can be a rock that crushes faith or a foundation on which it is built, but as we see in the novel and in Scorsese’s excellent film, it’s not a question worked out at a safe distance from suffering. Whatever answers exist, they are found in nakedness and pain, at the quiet end of all things.
Father Rodrigues misses the depth of the question in the relative safety of Catholic Portugal, but that changes when he and another priest sneak into Japan to look for Father Ferreira – their missing and possibly apostate mentor. The Japanese government, having observed that non-western countries which welcomed the church usually ended up overrun by the rest of western culture, has completely outlawed Christianity. There are no half-measures and, for the “faithful”, a violent end is sure. The Japanese Christians live in fear – both of the authorities and of their neighbors, as betrayal is financially rewarding – but have found ways to practice in the shadows. They welcome the priests wholeheartedly, but are put in fresh danger by their presence. The savvy and coldly effective governor of the region uses the villagers as leverage against the priests. Father Rodrigues, saddled with an “unworthy” companion and lost in the “swamp of Japan”, enters a spiritual echo chamber, where all he hears are cries of agony and his own prayers.
Your understanding about how things turn out will depend on your interpretation of the nuances in the story. There are no simple answers. Shusaku and Scorsese, both Catholic, do not play nice with the church, their faith or God. This is ruthless work, like fitting a camel thru the eye of a needle.