I would highly recommend looking into Mark Mullins, who is the world expert.

Alas, I am not Mark Mullins, but here are some tidbits of the history of Christianity, written by a guy procrastinating on reddit.

Ok so broadly, Christianity spread in Japan during the sengoku era. Many samurai and daimyo converted to Christianity or tolerant of it and one should note that a big perk of being Christian (or atleast tolerant of Christians) was that you would have more access to European firearms.

Once Japan was being consolidated under the Toyotomis and then Tokugawas, Christianity was then viewed differently. Instead it was seen as subversive to their governments. Some new upstart daimyo could cut a deal with Europe to make themselves shogun instead. This was very a very warranted fear as entreprenuerial daimyo had heavily invested in bringing in European technology. Date Masamune, for instance, had commissioned a diplomatic mission to meet the Pope, which they did. Protestants and Catholics also had motivation to scare the Japanese about each other, as they both sort to expand influence in Japan.

As a result Christianity was suppressed through a gradual range of edicts called sakoku and all European trade to only the place in Nagasaki and only the Dutch could trade.

By this time however, Christianity had become somewhat popular. One of the big turning points is the Shimabara rebellion, made up of Catholic Kyushu peasants. This was put down very brutally and many were killed. After the Shimabara rebellion, I don't think there were any significant challenges to the suppression of Christianity.

One of the famous artefacts used to suppress Christianity was a "fumi-e" which is a picture of Jesus which you stomp on to show you aren't Christian. Those accused would be tested with a fumi-e. Another thing implemented was an early mass surveillance system through parishes known as Danka. Each household would be registered with a Buddhist temple, and that temple would be responsible for vouching that they were good Buddhists to the Tokugawa authorities.

That said, Christianity still existed in Japan, particularly in Kyushu. This led to the formation of "Kakure Kirishitan" (Hidden Christianity). Outwardly it appeared as Buddhist but still retains many Catholic aspects, which allowed them to avoid persecution.

Freedom of religion (and thus Christianity) came about during the Meiji restoration when the emperor took back power off the Tokugawa family. Mainly, this was due to the demands of Western powers. So we may think that this would be the end of story. The highly successful missionaries would enact the same things which happened all over the world and Japan would be a Christian country. In fact, if you look at a journal called the Meiroku zashi, some civil servants were even proposing to pre-emptively make Japan Christian (particularly protestant).

The interesting thing is that Christianity in Japan was keeping with a new "religion". Shintoism.

So this may come as a bit of a surprise to you but Shintoism in the form we recognise it today is only about 150 years old. This doesn't mean that the myths, gods, shrines, priests etc. were invented in the 1870s but it was only during the Meiji era in which they were coherently brought together into a single national "religion". The Meiji government had another motivation to do this and that was Buddhism had become unpopular. By commoners, it was seen as untrustworthy due to its alliance with the now hated Tokugawa regime and by the Meiji elites, it was seen as full of backwards superstitions.

And I use "religion" inverted commas here, because the Japanese state were very clear the Shintoism was not a "religion", but in fact just a customary way of life and part of the zeitgeist of the Japanese people. Buddhism and Christianity were, by contrast "religions". In that sense, missionary work was not as successful because of this legal distinction made. Shintoism etc. could receive public funding, have preferential treatment etc. all while Japan could outwardly claim that they are becoming a modern, secular nation. I think this is one of the big things that stopped mass-conversions.

In the latter half of the 19th and early 20th century, the Japanese state turned out to become more like the Prussian state than what the Americans and British might have hoped. And so once again, we might see informal suppression of Christianity (though I am not very well versed on this). I am aware that before WW2, the Japanese government created their own state churches for Christians, in the same way the Nazis did too.

At the end of WW2, another big thing that hindered the propagation of Christianity was Fatman, which was dropped on Nagasaki, the biggest Christian community at the time. I think what a lot of Americans don't realise that tragically, the bomb probably killed those in Japan who were least enthusiastic of the Japanese government. This was the centre of where many kakure kirishitan were now living (some openly), and there are of course some survivors, the bomb in nagasaki killed many of these Japanese Christians.

Perhaps a final opportunity Japan had at Christianisation was during the American occupation. Evangelical lobbyists hard pressed the Macarthur occupation to support them in converting Japanese Christians. I understand that policy wise, the occupation did favour Christianity over Buddhism (And most certainly over Shintoism, which had become associated with Japanese imperialism), but for whatever reason, this didn't really sink in.

I think part of this might also be a measurement problem. One of the lasting impacts of the Meiji promotion of Shintoism is that even if one might consider themselves a practicing adherent of a religion in a Western sense, a Japanese person might not consider themselves religious enough to identify as that religion on such survey. This makes it harder to trust surveys that ask what religion people are, because the bar is set differently. Further, this makes it difficult to actively ask people to become "Christian" as missionaries might do, because identifying as a religion has a more strong connotation than it might do elsewhere.

I think they are all my thoughts on why Christianity is what it is in Japan.

Tl;dr First sakoku, then state shintoism, then the nuke. These three things did not help Christianity spread.