While there had been a flourishing trade with the outside world at times in the past, the ascension of the Tokugawa shogunate in 1603 gradually put an end to that. The Tokugawa shoguns recognized the need for trade and technology but were deeply suspicious of foreigners, and viewed Christianity in particular as a threat to the shogun’s authority. As such, outside trade was gradually curtailed until the Sakoku-rei or “closed-country edict” prohibited Westerners from entering, Japanese from leaving, and Catholics from existing.

A single area, Dejima Island in Nagasaki harbor, remained open to Portuguese and later Dutch traders, who were able to realize astounding profits of 50% or more at the cost of being confined to the small island and bound by a draconian set of procedural rules. But, as with the rest of the world, there were many adventurers from other areas—England, France, Scandinavia—who were unwilling to abide by those restrictions. After all, Japan had developed a taste for eyeglasses, firearms, astrolabes, coffee, chocolate, and other items that could only be obtained overseas.

The remaining Christians in Japan—persecuted, occasionally in open rebellion, and often driven underground—were a particularly lucrative source of income, as they had nowhere else to obtain crucifixes and weapons (and many of the illicit traders fancied themselves defending the faith in addition to making a profit). Their seamanship and swordpoints honed by the constant inter-European naval warfare of the period, these privateers were formidable smugglers.

Naturally, the Tokugawa shogunate was not helpless in the face of such unwanted foreign incursion. To maintain the fiction that Japan was inviolate, and to exercise the immediate death sentence the law proscribed for unauthorized foreigners on Japanese soil, the shogunate employed a network of coastwatchers and spies. Lucrative rewards were quietly offered for those who discreetly informed upon Catholics or those trading illicitly with outsiders, and specially-trained shinobi-no-mono retained by the shogun from the Iga and Kōga clans were dispatched to deal with such incursions.

During the great siege of Hara Castle during the Catholic-led Shimabara Rebellion in 1637-38, for example, European privateers supplied the rebels and engaged in gunnery duels with both Japanese ships and their shinobi-no-mono crews and Dutch vessels hired by the shogun. Though few records ever existed due to the illicit and clandestine nature of the struggle, quieter and small-scale actions would be contested between smugglers and shogunate mercenaries and troops for over a hundred years until the Napoleonic Wars at the turn of the 19th century.

And that, my friends, is how the long-standing enmity between pirates and ninjas came to be.

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