Historical Look at Silence
https://www.youtube.com/watch?v=P36zBCA_no0
Historical look at Christianity in Japan and why there were the persecutions. Basically it was a combination of Spanish Imperialism which used christianity to set up puppet rulers and a paranoid Shogun government fearful of outsiders and people inside their country.
The reason why people like Inoue were persecuting the Christians was due to the orders of the Shogun Tokugawa Iemitsu. He didn't start the persecutions but he had a rebellion occur under his rule in the same region where our two priests arrived a year later. The rebellion started over the excessive taxation and cruelty of a local lord but took on a Christian aspect. The rebellion was eventually crushed with ruthlessness but doing so had been both costly and embarrassing. It was thought the Portuguese aided the rebels so they were completely barred from entry so 2 Portuguese priests going into Japan right after this was rather idiotic. Instead of being just annoying missionaries of a prohibited faith they could have easily been seen as enemy agents fomenting further rebellion. In fact, in 1640 a Portuguese ship arrived begging to resume trade and that ship was burned and most of the crew executed.
What's interesting is the similarity of the Jesuits and some of the Buddhist sects at the time. The Christians were favored by some lords because the Buddhists had been meddling in secular affairs for centuries fighting each other and local lords while threatening the Emperor occassionally with their demands. You had religious uprisings of peasants, lower ranking samurai, and fighting priest from what was called Ikko Ikki and Iemitsu's grandfather fought them in his old domain.
The Jesuits gathered a significant amount of power to themselves in the Kyushu area which was reminiscent of the problem with the Buddhist sects. It didn't help that the Spanish and Spanish religious orders slandered the Portuguese and the Jesuits and vice versa.
The real big change in policy though was in 1600 when a Dutch (Protestant) ship arrived with a British pilot and they told the man who would become Shogun (Tokugawa Ieyasu) about the real situation in Europe and elsewhere. Ieyasu wanted to leave a stable country to his descendants and Christianity didn't fit especially as it was too closely tied in with European imperialism of the day. His grandson though was more fanatical and he effectively closed off the country something Ieyasu never would have done and ruthlessly persecuted Japanese Christians.
Anyway, despite the antagonist saying Christianity couldn't grow in the swamp of Japan (the same was said in a similar fashion with Buddhism a thousand years earlier), it really had more to do with politics internationally and domestically rather than a spiritual crisis.