Shimabara is a smallish town on a peninsular on the West side of Kyushu. You might want to pay it a visit en-route between Nagasaki and Kumamoto – the former is reachable by train, and the latter by ferry. I visited in 2013.
To get to Shimabara from Nagasaki, take a JR train to Isahaya, then exit into the station concourse, buy a ticket on the Shimatetsu line (it’s the right hand ticket machine, no English signage at all), then double back onto the JR platform and you’ll find the Shimatetsu line on the far left platform. It’s a tiny, old-fashioned train that rumbles through the countryside to Shimabara (not the terminus stop, so listen out).
Shimabara has a big castle (pictured at the top) and an interesting history – the area was once home to a significant Christian population, and the related Shimabara Rebellion (1637-8, good summary here). Inside the castle there’s a museum with loads of related artefacts, including some interesting Christian symbols disguised as buddhist ones dating from the era of Christian persecution (many were killed, some were hurled into the nearby boiling-hot springs).
And speaking of hot springs: looming over Shimabara is an enormous volcano – Mt Unzen. It’s an impressive sight, but a worrying one – in 1792 it erupted, causing a megatsunami that shot across the bay, laid waste to the other side, then bounced back to hit Shimabara again – total death toll over 15,000. The last major eruption, in the 1990s, was also fatal.
From Shimabara a couple of ferries, some faster than others, run across the short hop to Kumamoto – you can see land quite easily across the water. You should be able to get acrosss without too much trouble unless – like me – you attempt this in typhoon season. An incoming storm meant that all boats were cancelled – if that happens to you, your options are to wait overnight or attempt a long train journey around, so I’d check the weather reports before making the trip this far (although that didn’t help me).