In Nagaski there are two important memorials that are actually Catholic related. The first is Urakami Cathedral also known as St. Mary's Cathedral. This Church is extremely interesting because of its history before the bomb, during the bombing, and after the bomb. I found some information online (thank you wikipedia)so I could explain it well: the construction of the Church began in 1895 after the long standing ban against Christanity was lifted. In 1865, the French priest Bernard Petitjean discovered that almost all the Urakami villagers were Christian. Between 1869 and 1873, over 3600 villagers were banished. During their exile, 650 died martyrs. The persecuted Kakure Kirishitan (Hidden Christians) came back to their home village from 7 years exile in 1873, and decided to construct their own church.
They purchased the land of the village chief where the humiliating interrogations had taken place for two centuries. The annual "fumie" interrogations required those present to tread upon an icon of the Virgin Mary or Jesus. They thought the place was appropriate considering their memory of the long persecution. Construction of the building was started by Father Francine and was completed under the direction of Father Regani. The frontal twin spires stood 64 meters high were constructed in 1875. When completed in 1925, it was the largest Catholic church in East Asia.
When the atomic bomb was dropped it detonated 500 meteres from the Cathedral. A replacement was built in 1959, after a serious debate between Nagasaki city government and the congregation. The city government suggested preserving the destroyed cathedral as a historical heritage, and offered alternate site for a new church. However, Christians in Nagasaki strongly wanted to rebuild their cathedral on the original place for their historical reasons. The place is a symbol of the persecution and their suffering. In 1980 it was remodeled to more closely resemble the original French style. It was beautiful inside; however, I couldn't take pictures inside!
This is all that is left of the original Cathedral. 
The second Catholic Memorial in Nagaski is the Memorial to the Martyrdom of the 26 Saints of Japan. On February 5, 1597, twenty-six Christians – six European Franciscan missionaries, three Japanese Jesuits and seventeen Japanese laymen including three young boys – were executed by crucifixion in Nagasaki on the orders of Hideyoshi Toyotomi. They were raised on crosses and then pierced through with spears. Persecution continued sporadically, breaking out again in 1613 and 1630. On September 10, 1632, 55 Christians were martyred in Nagasaki in what became known as the Great Genna Martyrdom. At this time Catholicism was officially outlawed. The Church remained without clergy and theological teaching disintegrated until the arrival of Western missionaries in the nineteenth century.
