Shimabara is a castle town on a peninsula in the far south-east corner of Nagasaki Prefecture, on the flanks of Mt. Unzen, an active volcano dominating the region. After nearly 200 years of dormancy, Mt Unzen last erupted in 1991, killing 43 and devastating the southern district of town with the resultant pyroclastic flows.
The city is also the site of the Shimabara Rebellion in which Christians and locals who were unsatisfied with grossly high taxes and oppression of Christianity fought to regain control of the territory. They were unsuccessful, and with the help of the Dutch, the Japanese stopped the rebellion and beheaded approximately 37,000 Christians and peasants. It also led to the ousting of the Portuguese who they no longer trusted, making the Dutch the only Europeans the Japanese were willing to trade with. Although Christianity had already been banned prior to the rebellion, the rebellion made the government even more anti-Christian and even stricter enforcement of the religious ban was established.
Nowadays Shimabara acts as the gateway between Nagasaki and Kumamoto and sightseeing in the Unzen Volcanic Area Geopark.
Trains run direct from Isahaya, near Nagasaki along the private Shimabara line. Note that as with many private lines in Kyushu, the Shimabara line departs from a slightly hidden platform zero within the JR station. Don't leave through the JR gates, just hop on the train and buy your tickets from the driver.
Various ferry options will let you reach Shimabara from neighbouring Kumamoto.
Ocean Arrow will take you from Kumamoto Port (熊本港) to Shimabara Port (島原港) in 30 minutes. One way is ¥800, a round trip ¥1520. Buses from Kumamoto city centre station to Kumamoto port are ¥480 one way (¥420 from the JR station). Note that the ¥1800 discount round trip special including connecting bus fare only runs from Shimabara -> Kumamoto -> Shimabara, and not reverse rendering it utterly useless for a tourist. The last ferry back to Kumamoto leaves at 7:20 pm.
The cheaper Kyusho Ferry (九商フェリー) will get you from Kumamoto Port (熊本港) to Shimabara Port (島原港) in 60 minutes but for a mere ¥680 or ¥1000 round trip. The connecting bus to the Kumamoto city centre course will still set you back ¥480 (¥420 for the JR station) each way. The last ferry back to Kumamoto leaves at 6:55 pm.
Although primarily designed to get Nagasaki residents to the Greenland themepark, an alternate option does exist to the north. For ¥430 each way, Ariake Ferry (有明フェリー) will give you a 45 minute ride from Nagasu Port (長洲港) just north of Kumamoto to Taira Port (多比良港) just north of Shimabara. Last eastbound ferry leaves at 8:00 pm.
Limited bus services exist around town and run approximately hourly servicing the three main areas of castle / central train station, the port, and the southern part of town with stops about a 10 minute walk away from the disaster hall and another right outside the Mizunashi-honjin Fukae road station (see below).
Note that although some run close, none actually go up to Unzen Geopark itself.
As the various attractions are each about 3 km from the port, if coming by sea, walking around town may be a desirable option. However, despite Shimabara's beauty, like most Japanese cities, much is a desolate ferro-concrete urban wasteland, in this case a thin strip bordering the highway that runs directly through town. If you do choose to walk, the route between the port and the castle could potentially be quite pleasant if one were to carefully avoid said main highway and weave their way north.
Consider the following course:
From the Port to Sengen Park and Ashiyu Footbath and then work their way to Hirobaba via the coast.
From here take a wander down the little old-fashioned residential alleyways to Hamanokawa Spring.
Cross briefly west across the nasty highway district towards Shirachi Lake (beware of the unusually crazy drivers), perhaps enduring a little more of it to make a brief detour via the beautiful carp stream.
Make your way to Yutorogi Ashiyu Footbath and finally the castle via the temple district.
Shimabara Castle (島原城) is an unusually striking castle reconstruction due to its regular, tall yet almost pyramidal, design. Furthermore, it is rather unique in that the town has clearly chosen functionality over form and forgone the usual garden in favour of placing a carpark within the castle plateau itself. Urgh. One can literally park 5 metres from the door. Despite this, the thin terraced gardens behind the castle, overlooking the ocean are packed to the brim with hydrangeas and really pretty.
Mt Unzen Nature Park (Unzen Volcanic Area Geopark). The main attraction, but bring a car.
Mt Unzen Disaster Memorial Hall. A museum roughly 3 km south of the port. Covers a variety of topics based upon the destruction of southern Shimabara by pyroclastic flows from Mt Unzen's eruption and future disaster prevention. Admission ¥1000 for adults.
Ever get that sinking feeling?
Mizunashi-honjin Fukae Road Station. Besides 水無川 on Route 251. Roughly 4 km south of the port and walking distance from the Memorial Hall. At first glance, this may just appear to be an ordinary road rest station for long distance drivers (try not to get hung up on the apparent contradiction that this road doesn't actually lead anywhere further south from here) but beneath this facade it hides easily the most unique tourist attraction in town and unusual even by Japanese standards -- yet it mysteriously does not even appear as one of the dozen dots on the local tourist guide map. After the southern side of town got sacked in 1991, 11 of the original houses from the time were preserved here in their half-buried awe. Roughly half are outdoors in a park setting and the other half enclosed in a sort of greenhouse so you can get a good view regardless of the weather. Although at first a pile of rooftops on the ground might just look like the plethora of collapsed houses in rural Japan try to bear in mind that the entire house is still there, in one piece but just buried, and were buried in an amazingly short period of time by pyroclastic flows from a volcanic eruption. Information exists in English, Japanese, Korean. Being a road station, a pile of restaurants and a fruit stand exist so its also a convenient place to pick up lunch. Admission free.
Hara Castle Ruins. Hara Castle was the Christian stronghold during the Shimabara Rebellion. It was attacked by the government with help from the Dutch who were trying to gain favor with the Japanese and get rid of the Portuguese, which they succeeded in doing. Nothing remains of the castle itself, but the foundations are clearly visible and some remnants from the rebellion are still visible.edit
Visit the various natural springs around town. These are scattered around town and consist of no less than two free footbaths (one opposite the port and one a few blocks south of Shimabara Castle), many nice onsens (admission prices variable) and a pile of drinkable water springs (some quite hot!) including some with what appear to be sectioned runoff ponds for various forms of domestic clothes washing or fish clea... they're still all marked on the tourist map regardless!
From Nagasaki to Unzen, the bus leaves at 9:00, 13:00 and 16:00 and takes 1h40. The schedule is the same for coming back. One-way is 1900¥ and round-trip is 3420¥.
If you want to go to Shimabara from Unzen, the bus leaves at 16:13, 17:13 and 18:16. There are other buses before and after. It takes 45 minutes to reach Shimabara and costs 750¥. If you want to catch the last ferry to Kumamoto, you need to take the bus at 16:13. The bus drops you in front of the ferry terminal.
There are 2 ferry companies. One ferry leaves at 8:25, 10:15, 12:05, 13:50, 15:45 and 17:30.