A reply to /u/JOHNOLIVER2016

This is a complex, multi-faceted question, and unfortunately there is no single book that can answer it. If you really want to study this in depth, I suggest two starting points.

First is to compare the strength of the Portuguese versus other emergent powers, in particular the Dutch, in the Indian ocean and in South China Sea.

Second is to look at the nature of the internal conflict in Japan, and of other powers in that region.

For the first point, it is very important to note that the expansion of the Portuguese empire around the world did not lead to strength back at home. In 1578, King Sebastian of Portugal hastily undertook a crusading campaign in North Africa at age 21, resulting in the massacre of the expeditionary army and of much of the aristocracy and nobility inthe Battle of Alcácer Quibir. He died without an heir, and many of the potential successors perished with him. The resulting regency period was unstable and eventually led to King Philip II of Spain asserting his claim and bringing Portugal under personal union with Spain. This had significant strategic consequences for the Portuguese, including their entry into Spain's orbit and inheritance of Spain's enemies, most notably the Dutch.

The Spanish and Portuguese had set up separate routes for exploration and trade, based on the Treaty of Tordesillas. The area around South East Asia and Japan were where the lines were literally fuzzy, partially due to inability to determine latitude accurately. Thus, while the Portuguese Jesuits arrived in Japan first, Spanish Mendicants followed not long after through the Pacific ocean route. While they were in theory both Catholics, they had some level of rivalry that fluctuated with time.

Fundamentally speaking, Portuguese presence in the east Indies had always suffered from lack of numbers. The expeditions were run directly by the King, who hired merchants and mercenaries to provide and operate the vessels. This is why the Portuguese Jesuits became involved in local ventures and key trades in order to finance themselves.

At the same time, Dutch vessels had themselves started to enter the Indian ocean and South China sea, and as early as 1605 they had wrested Amboina away from the Portuguese and attempted to capture Malacca in 1606. This led to significant weakening of Portuguese position in the Indian ocean and South China Sea.

This is the larger "Europe-to-Asia" picture through which you should view the Suppression Order Against Jesuits when it was promulgated in 1597.

For the second point, Toyotomi Hideyoshi had risen to become the strongest daimyo of Japan following a period of civil war, but he never earned the title shogun. Instead, he was able only to make himself the imperial regent. While he was strong, he had to cultivate a careful approach to possible rivals, many of whom were in the south and west areas of Japan. Thus, it makes sense that he saw the Jesuits (and Christians in general) as potential rivals, or at least that they may align with his rivals. On the other hand, this gave the Christian daimyos very little space to maneuver, as the sum of their powers were weaker than Hideyoshi's. After all, he had just won the civil war.

Tokugawa Ieyasu largely followed the same lines of suppression of Christians, however he had a stronger rule than Hideyoshi. It is incorrect that there was no plan for armed resistance, however it all went to naught as neither Spain nor Portugal could support one meaningfully. Tokugawa increased the level of suppression until the 1630s, a period that saw some upheavals due to a mini ice age. One outcome of the religious conflict in Europe of this period, the Thirty Years' War, was the secession of Portugal from personal union with Spain. Back to Japan, the shogun was able to leverage Dutch willingness to literally bow their heads to shogunate demand for subservience and severe limitations on trade, unlike the Portuguese and Spanish who refused to do so. Thus started the period of Sekoku as we know it. The intra-Asia trade, in particular the link to Japan, was a very vital part of the Dutch VOC's trading system.

So in summary, both Portugal and Spain were either in a weak position or in conflict with each other, and locally the Christian daimyos had no chance to stand up against the imperial regent nor the shogun.