Blessed with a breathtaking location, Nagasaki is strung together on a long series of hillocks in a scenic valley that follows the arms of the Urakami River down into a gentle harbor. Unlike Hiroshima, the city was left with no suitably intact reminders of the atomic bombing, and perhaps for this reason, there were apparently no compunctions about rebuilding the town right up to the edge of a tiny ground-zero circle with a stark steel monument at its center. Yet as relatively new as everything here is, Nagasaki's international history shows through, from lively and compact Chinatown to the European-style mansions and Catholic churches on the hillsides.
In the mid-16th century, Portuguese missionaries, including Saint Francis Xavier, came ashore to preach Christianity throughout Kyushu. This new and altruistic religion—coinciding with the arrival of firearms—threatened to spread like an epidemic through the impoverished and restive masses of the feudal system. In 1597, to give bite to a new decree by Chief Minister Toyotomi Hideyoshi to stifle worship, 26 followers were publicly crucified in Nagasaki, an act that brought condemnation from the world. This cruel and shocking display was followed not long after by Tokugawa's nationwide edict making the practice of Christianity a capital offense.
All foreigners were expelled except the Dutch, who, considered to be lacking overt propensities to convert anything but profits on trades, were sequestered on an island, Dejima. Of the local population, only merchants and prostitutes were allowed direct interactions with them. The Dutch took over the considerable trade brokering between China and Japan formerly done by the Portuguese. Though the rest of Japan was strangled by isolation and starved for foreign goods, Nagasaki continued to prosper by making use of this tiny but important offshore loophole in the Tokugawa anti-trade policy out in the harbor. This arrangement lasted until 1859, when insular Japan was forced to open up to the outside world.
Once other ports became popular, the city's status diminished. Centuries later, Mitsubishi decided to concentrate its arms manufacturing and shipbuilding capabilities here; the industrial presence and bad weather over the primary target of Kokura in northern Kyushu made Nagasaki the site of the second atomic bomb drop in 1945.
The city isn't small, but it occupies a long winding valley, so you can experience it in manageable increments. Similarities with San Francisco are frequently noted. The comparison is not far off, though the posters advertising whale-bacon and manga remind you of where you are. Most of the interesting sights, restaurants, and shopping areas are south of Nagasaki Station, but the Peace Park and the Atomic Bomb Museum are to the north, about 10 to 15 minutes by streetcar or taxi.