Five eras, 21 moments. Scroll sideways through the timeline.
The Christian century begins
Bans, martyrdoms, uprising
Faith kept in secret
The hidden step forward
Freedom and a living Church

Francis Xavier lands at Kagoshima on 15 August with Anjirō and two Jesuit companions.
Xavier preaches in Hirado, Yamaguchi and Kyoto and is received in Bungo.
Ōmura Sumitada is baptized, the first daimyo to become Christian.

Portuguese ships begin calling at the new port of Nagasaki.
Four young Japanese envoys, the Tenshō embassy, sail for Europe and Rome.
Toyotomi Hideyoshi issues an edict expelling the missionaries.

Twenty-six Christians are crucified on Nishizaka Hill, Nagasaki, on 5 February.
The Tokugawa shogunate bans Christianity nationwide; Takayama Ukon goes into exile in Manila.
The Great Martyrdom of Nagasaki (Genna).
The Shimabara–Amakusa uprising ends at Hara Castle.

Portuguese ships are barred; Japan enters its closed period and the faith goes underground.

On 17 March Hidden Christians from Urakami reveal themselves at Ōura Church.
The fourth Urakami persecution: over 3,000 Christians are exiled across Japan.
The public notice boards banning Christianity are removed.
Urakami Cathedral is completed by the returning community.
The atomic bomb destroys Urakami Cathedral on 9 August.
Pope John Paul II visits Nagasaki.
188 Japanese martyrs are beatified in Nagasaki.
Takayama Ukon is beatified in Osaka.

UNESCO inscribes the Hidden Christian Sites in the Nagasaki Region.
Pope Francis prays on Nishizaka Hill and celebrates Mass in Nagasaki.
Dates from UNESCO, Wikipedia and standard references; see each place page for sources.