It's often interesting to look into different belief systems. A visit to Magome Catholic Church is a wonderful way to learn about one of the local religions.
You're spoiled for sightseeing choice when spending time in Nagasaki. Magome Catholic Church is a good place to begin here, but there are many other interesting spots to appreciate. Glover Garden, Oura Church, and Confucius Shrine are close to the house of prayer and will fill in your day nicely.