If you are interested in the Christian history of Japan, then you should probably visit Nagasaki. In Minami-Shimabara city, Nagasaki Prefecture, there are the remains of Hara Castle, which was the site for the Shimabara Rebellion. The Shimabara Rebellion was a big historical event in Japan, in which Christian peasants rose up against the Arima Clan and Government forces in 1637-38. This event led to Japan closing the county to the outside world for over 200 years. The ruins of Hara Castle were designated a World Heritage Site for Hidden Christian Sites in the Nagasaki region in 2018. However, very few of these sites remain today.
To understand and learn more about the Shimabara Rebellion and Minami-Shimabara's Christian history, you should visit the Arima Christian Heritage Museum near Hara Castle. I would recommend visiting this museum before going to the remains of Hara Castle, since it will help you understand the history of the Shimabara Rebellion better. The museum opens from 9am to 6pm, and closes on every Thursdays and during New Year Holidays.
When you visit Hara Castle, don't forget to drop by the visitor's center near the Honmaru area, (the area towards the center of the castle) . From here you can rent VR tablets for free in various languages. You can also use your own smart phone to download the app called "Street Museum" where you can use the VR tour for free! The site of Hara Castle is huge and it is a bit of a walk to get to the Honmaru area. In addition, there is no parking lot. However, there is a shuttle bus or you can rent a bike, in order to get to the Honmaru area. You can rent an electric bike for free from the Harajo Onsen Masago and Arima Christian Heritage Museum. This is a nice way to explore Hara Castle where you can see some beautiful views.
The Minaimi-Shimabara area offers more activities, such as beaches and dolphin watching tours!