One thing to consider is the context in which this happened. Europeans arrived in Japan during the "warring states" period (about 1467 to 1603), when the country had no unifying military leader (there was an emperor but his power was largely religious and symbolic) and no unifying political structure. Many different lords (daimyo) fought for ascendancy to rule over all of Japan. Into this context arrived Europeans, who possessed wealth and power and weaponry heretofore unknown in Japan. Allying with Europeans meant adopting their religion, which then led to obtaining guns and various other things that would benefit the daimyo in his military efforts. Such benefits led to lords of different regions converting and having all of the people living in their region also converting at the same time.

This warring states period was brought to a close when one particular daimyo, Tokugawa Ieyasu, succeeded in subduing all opponents and uniting the nation under his control as shogun. His base of power was in Edo (now Tokyo, in eastern Japan). Christianity had its greatest influence and power over those living in Western Japan, which is the part of Japan closest to mainland Asia and the part where Europeans mainly landed. In other words, the Tokugawa Shogun was not one of the daimyo who had ascended to power using a lot of European influence, guns, technology, and allies. He saw European influence, guns especially, as a threat to his rule over Japan, which was fragile early on. He was very skilled at seeing dangers to himself and his rule and acting against them quickly. To prevent threats to his power from daimyo who were gaining outside help from Europeans, he banned guns in Japan and he banned people from leaving Japan or foreigners from coming to Japan (with the exception of limited trade that was conducted on an offshore island). He also banned Christianity, since it was inextricably tied in with these external threats such that interest in or ties to Christianity were tantamount to treason because it meant you'd now have access to weapons and allies that Tokugawa Ieyasu did not. Tellingly, the one European country that Tokugawa Ieyasu allowed to continue to trade with Japan (on the artificial island of Deshima that was created solely as a place for trading, in Nagasaki Bay) was the Netherlands, which did not seek to convert people or gain allies to its own international colonization efforts, but just wanted to trade.

I should mention that while Christianity began in Japan as inextricably linked with global power and colonization, once Japan's isolationist policies became cemented in place, there remained Japanese Christians who were cut off from these issues, and remained Christian due to faithfulness to the religion. They ended up being oppressed and had to worship in secret. The religion changed quite a bit in Japan over the next 250+ years, with indigenous ideas and practices added to it. Now that it's OK to be Christian in Japan, though, there's virtually no interest in it and missionaries have had little success.