Note that this route is dependent on being able to catch two short (~30 minute) ferries: the first from Kuranomoto to Ushibuka on the main Amakusa island, and the second from the top of that Amakusa island to the mainland just down the coast from Shimabara (specifically, from Oniike to Kuchinotsu). Typhoons or other weather events can affect the ferry schedules and may even cause cancelation of service, so plan carefully; if you’re on one of the Amakusa islands and the ferry service is canceled, you’re stuck there until it resumes, unless you want to take a very long detour (see below). Also note that there are lots of other ferries going to and from islands in Kyushu, so you can adjust your route accordingly. For example: if you have your heart set on seeing Kumamoto and its famous black castle, there’s a ferry that goes directly from Shimabara to Kumamoto. You could take that one over, and return via the Ariake ferry that goes from a point farther up the coast back west to a point north of Unzen on the route to Nagasaki (the one mentioned in the North Kyushu route). Alternately, you could see Kumamoto as part of the main across-Kyushu route, as a short detour from Mt. Aso.
One more thing. Although we’ve warned you about ferries being canceled in the event of a typhoon, it’s important to note that, somewhat surprisingly, the Amakusa islands are NOT completely cut off from the mainland. The islands are very close to one another and are connected at the city of Amakusa, and the eastern island is also connected to the Kyushu mainland via a bridge. (So ferry access is only important if, as in the case of this route, you’re traveling to the western island first.) Therefore, if you wanted to cycle through both islands, you could skip the second ferry to the mainland and simply cycle down to Amakusa City and from there to and across the smaller eastern Amakusa island, and then go from there to the mainland (via the bridge on the Amakusa Pearl Line). Of course, this puts you very far from Nagasaki, but very near the city of Kumamoto, so you could end your trip there and turn the route into a Kagoshima to Kumamoto route.