In fact it was the Dutch not the Portuguese who maintained this precarious commercial tie with the locked-down Tokugawa Shogunate.
The Dutch came to Nagasaki for Japanese copper. Each season a handful of them were allowed to disembark at Dejima, a purpose-built artificial island in the city's harbour, roughly the size of half a football pitch. (200x80 paces with around 25 techos.)
There they resided with their Malay slaves, generally interacting only with locals belonging to hereditary classes of officials, interpreters and courtesans. Dejima was linked to the mainland by a bridge, sealed at both ends by locked gates. Only the most senior of the Dutch could cross this to the Nagsaki itself, where they negotiated with the Shogun's local governor every year.
The novel takes us first to the Dejima of 1799, when just two Dutch ships were permitted to turn up there each year. This marks the start of the period when, for fifteen years, Dejima was the last place on earth where the Dutch flag was flying, as the British had overrun the south-east Asian colonies and the Netherlands themselves had been occupied by Napoleon.
Dejima is one of three enclosed locations which define the action of Mitchell's novel, the others being a hilltop nunnery and an intruding British ship. Yet it is arguably this tiny trading post that provides the raison d'être for Mitchell's experimentation with the historical novel, for the peculiar nature of this cultural and commercial bottleneck between east and west underlies almost everything that the book has to say of interest to the modern reader.
The location is in a sense a crucible of modern, progressive ideas, different aspects of which Mitchell embodies in his lead characters, such as Dr Marinus and Jacob de Zoet himself, who is tellingly provided with a prim and pious protestant outlook in spite of his obvious rationalism and latent liberalism. It also affords the author opportunities for some of his best comic moments, such as the bold statement of the governor of Nagasaki that coffee would never 'take hold' in Japan.
Yet it's altogether easier to pack these limited, claustrophobic enviroments with stereotypes than it would be if his gaze extended much beyond the land bridge into Nagasaki itself. Mitchell lived in Japan for eight years and married a local girl, which is why I naturally expect him to have the same developed fascination with life on the ground there as I do, yet what we mostly get is a rather hackneyed environment occupied by the inscrutable easterners of western cliché.
There is one extraordinary chapter opening (location 6176 on my Kindle edition) where Mitchell delivers a much more voracious and yet carefully-observed account of Nagasaki life, set within a top-notch prose poem. But I found myself interpreting this as a planned compensation for the novel's pervasive sketchiness.
The depraved cultish convent of Abbot Enomoto on the other hand is probably intended to resonate strongly with modern Japanese pop-culture sensibilities and not as a realist representation of Shinto heresies of the time. One critic has compared the abortive Samurai rescue mission to a take from anime, and the chapter covering Orito's escape attempt read like the action within a fantasy computer game for me.
The story of H.M.S. Phaeton, the Royal Navy 5th-rate ship of the line which engages Dejima in the book's third section has been lifted from the historical record, albeit with a degree of temporal displacement. This incident may help answer the question which has often occurred to me — why it was the American fleet under Admiral Perry which ended Japan's isolation and not the British.