So God sure ended his silence in style, huh?
Let's rewind a bit. Rodrigues ended up apostatizing to save the lives of Japanese Christians, stomping on the fumie and renouncing his faith. Why? It's simple: "for love Christ would have apostatized [...] even if it meant giving up everything he had" (8.100). In Rodrigues's case, that means sacrificing his reputation, his religion, and his homeland. Though it hurts him, Rodrigues knows he made the right choice, because he can hear Jesus telling him to trample away.
With that, Rodrigues is renamed Okada San'emon and made a Japanese citizen. That's when Kichijiro shows up for the gazillionth time begging forgiveness—but something is different this time. This time, Rodrigues is able to realize something that he should have realized all along—that he's as much of a Judas as Kichijiro. At the same time, he also realizes that Jesus still loves both of them, just as he had loved Judas, the man who betrayed him.
Ultimately, Rodrigues forgives Kichijiro—not to mention himself. Although he might not ever return home to Portugal or step foot inside a church again, he'll always have a piece of the faith alive in his heart.