Christianity was introduced to Japan in 1549 by Francis Xavier. He said the Japanese were the 'joy of his heart' and 'the best we have yet discovered'.
The real founder of Japanese Christianity was Allessandro Valignano in 1579 who had a vision of a Christian Japan acting as a springboard for missionaries throughout Asia. To do this he creared seminaries and formed native Japanese clergy.
Japan quickly became the most succesful mission in all of Asia with a Christian population estimated at 300 000 (out of about 15 million Japanese), with prominent Daimyo converts and Christians as important advisors of the most powerful man in the land, Toyotomi Hideyoshi.
However it was not to last. Hideyoshi already began to distrust Christianity and his successors, the Tokugawa Shogunate, banned it outright. They forced all Christians to abjure their religion or be tortured and killed, initially to be burned or to be hung upside down in dung, later via crucifixion.
A test was instituted where you had to trample an image of Jesus, the Fumie, to prove you weren't Christian.
The European missionaries all fled, but the native church endured. Japan was closed off to all foreigners except a small Dutch station at Nagasaki, because the Calvinist Dutch had no problem trampling on Icons.
Famously the executions became a spectacle where the executed people said Sayonara and then the crowds watching would sing Catholic Hymns in response like the Magnificat or Laudate Omnes Gentes.
The Shogunate then changed tack and tortured them until they apostasised from the religion so that no such spectacles could take place.
The Japanese Church was forced underground, becoming the Kakure Kirishtan, or hidden Christians. They made statues of the Virgin Mary that looked like the goddess Kanon or hid crosses behind Buddha statues and continued to practice their faith in secret.
There was one attempted uprising called the Shimabara Rebellion, but this came to very little.
This hidden Christian community endured until westerners opened Japan again in 1854. They came out of hiding in 1865 when a French consulate built a small chapel which was suddenly engulfed by a large population of Christians no one knew about, asking to be blessed and joining Mass.
The Christian population was incidentally concentrated in Nagasaki, so that a major proportion of Japanese Christianity was blown up by the Atom bomb in 1945. The Japanese had thought that their presence was maybe why the US was not bombing Nagasaki so heavily, but the Atom Bomb incinerated a large percentage of them. There is a famous picture of the burnt out husk of Nagasaki Cathedral.
The history of Christianity in Japan is very sad. There is a good book by Shusaku Endo called Silence, which tells the story of the Hidden Christians.
A famous passage talks of where a Christian confesses to having trampled on a Fumie, an Icon of Christ:
"I too, stood on the sacred image. For a moment this foot was on his face. It was on the face of the man who has ever been on my thoughts, on the face that was before me on the mountain, in prison, in all my wanderings, on the best and most beautiful face a man can ever know, on the face of him who I longed to love. Even now the face was looking on me with eyes of pity from the plaque rubbed smooth by many feet. 'Trample!' said those compassionate eyes. 'Trample! Your foot suffers in pain; it must suffer like all the feet that have stepped on this plaque. But that pain alone is enough. I understand your pain and suffering. It is for that reason that I suffered, for that reason that I am here'."
As to your other questions:
Japan was centrally controlled and stable and its leadership realised they must rapidly adapt to the West or they would fall prey to it. The miracle of Japanese Industrialisation has never been equalled, where a feudal mediaeval society became modern and Industrialised to the level where they could beat a major European power, Russia in 1905, in the matter of 40 years. This is why it was never colonised except for the American occupation from 1945-52, which may arguably be one.
Shinto teaches that everything is one Monistic unity, with emanations of that unity of differing powers. The most powerful are Kami, loosely termed gods in translation, but this is a poor equivalent. Some Kami like Amaterasu the Sun goddess look very much like we would think a polytheistic god should, others are just rocks or trees and historically the Emperor himself was considered a Kami.
Shintoism was the traditional religion of Japan based on their ancient myths and has multifarious approaches and ways.
Its idea of Monism works well with Buddhism, which is why Buddhism established itself so early in Japan as well.
Christianity arguably did well in Japan initially because the Idea of the Incarnation of God as Jesus makes a lot of sense out of a Shinto viewpoint of Musubi or expression of power and the idea of God sacrificing himself for man works well with traditional Japanese ideas of loyalty and sacrifice unto death. This is only a theory though and Nationalist Japan continued to suppress Christianity after Japan was opened in favour of the Native State Shinto religion. After WWII when this was no longer the case, the bulk of Japan's Christians had been incinerated. This is one of the reasons why there are so few Christians there today.
