When Father Rodrigues first arrives in Japan, his head is filled with idealized visions of the country. Though Christians are currently being executed en masse in Japan, Rodrigues is confident that their glorious martyrdom won't go by unnoticed by the man upstairs.
Except it does.
As Rodrigues himself states: "in the face of this terrible and merciless sacrifice offered up to Him, God has remained silent" (4.47). In this way, God's silence becomes a reflection of Rodrigues's growing doubts, not only due to his internal struggles but also due to the seemingly meaningless deaths of countless Japanese Christians. Though God does indeed break his silence by the end of Silence (har har), it's not quite in the way Father Rodrigues expects.