A young boy has lost his mother and is losing touch with his father and the world around him. Then he meets Hesher who manages to make his life even more chaotic.

Intent on investigating the truth behind Father Cristovão Ferreira's abrupt end of correspondence, the devout Portuguese Catholic priests, Sebastião Rodrigues and Francisco Garupe, set off to Japan, in 1633. In great disbelief, as the rumours of Ferreira's apostasy still echo in their minds, the zealous Jesuit missionaries try to locate their mentor, amid the bloodshed of the violent anti-Christian purges. Under those circumstances, the two men and the Japanese guide, Kichijiro, arrive in Japan, only to witness firsthand the unbearable burden of those who have a different belief in a land founded on tradition. Now--as the powerful Grand Inquisitor, Inoue, performs hideous tortures on the brave Japanese Christians--Father Rodrigues will soon have to put his faith to the ultimate test: renounce it in exchange for the prisoners' lives. There, in the ends of the world, a subtle change has begun; however, why is God's silence so deafening?