The tax collector had done it before. In the domain of Shimabara on Kyushu's western peninsula, the methods for extracting payment from people who had nothing left to give had been refined over years of practice under the Matsukura lords. 松倉重政 (Matsukura Shigemasa) and his son 松倉勝家 (Matsukura Katsuie) had taxed their domain to the bone to build a new castle and satisfy ambitions the land could not support. Seven consecutive poor harvests between 1629 and 1636 had left the peasants with nothing. In autumn 1637, the Matsukura demanded seven years of back taxes all at once.

The collection methods were inventive in their cruelty. There was the 蓑踊り (mino odori) — the "straw raincoat dance" — in which a debtor was wrapped tightly in straw and set alight, forced to thrash and roll to put out the fire. There were public beatings. There were extended incarcerations in winter cells.

And then, near the end of November 1637, a tax collector arrested the pregnant daughter-in-law of a village chief and tortured her to death. Her father-in-law and her own father did not deliberate. They rose with approximately 700 men immediately.

The fire spread fast. On December 17, 1637, rebel forces assassinated the local 代官 (daikan) — the magistrate Hayashi Hyōzaemon. With the magistrate dead, the domain's administration ceased to function overnight. The rebellion had a date, and a name: Shimabara.

The uprising found its center of gravity in a boy. 天草四郎 (Amakusa Shirō), also known as 益田四郎時貞 (Masuda Shirō Tokisada), was born around 1621 to Masuda Jinbei, a former retainer of the Konishi clan — a Christian daimyō family that had been dispossessed after Sekigahara in 1600. Shirō was approximately fifteen or sixteen when the rebellion began. Before it started, he was already famous in the underground Christian communities of Kyushu: people said he had walked on water, called birds to his hand from the sky, and healed the sick. His followers proclaimed him 天地さん (Tenchi-san) — Heaven's Messenger. Whether he commanded battles or served primarily as a living symbol for experienced 浪人 (rōnin) generals to rally behind remains uncertain, but his presence transformed a tax revolt into something that felt, to its participants, like a holy war.

Rebels from the Shimabara Peninsula and the nearby 天草 (Amakusa) Islands converged on the ruins of 原城 (Hara-jō), an abandoned fortification on the peninsula's southern tip. Approximately 37,000 people gathered inside its walls — fighters, their wives and children, Christian sympathizers who had nowhere else to go. Their banners carried Portuguese inscriptions: "Louvada seia o Santissimo Sacramento" — Praised be the Most Holy Sacrament — along with images of the Virgin Mary and the cross. In the shogunate's heartland, 37,000 starving people announced their faith in a foreign language and waited.

The Tokugawa shogunate's response was overwhelming and embarrassing in equal measure. It ultimately mobilized over 125,000 troops — an astonishing number to besiege a single abandoned castle — and still found the first months of the siege going badly. The first commander sent to end it, 板倉重昌 (Itakura Shigemasa), was killed in an ill-judged assault on January 1, 1638. He was the only senior shogunate commander killed in battle during the entire Edo period.

In desperation, the shogunate requested military assistance from the Dutch East India Company. The Dutch Opperhoofd Nicolaes Couckebacker personally accompanied the warship de Ryp to a position offshore. Dutch cannons were mounted in a shore battery and bombarded 原城 (Hara-jō). The bombardment proved largely ineffective. The rebels sent mocking messages to the troops besieging them. The Dutch withdrew after about two weeks, quietly humiliated.

The castle finally fell on April 12, 1638, after nearly four months of siege, when the defenders ran out of food and ammunition. 天草四郎 (Amakusa Shirō) was executed — approximately sixteen or seventeen years old. His head was taken to Nagasaki for public display. An estimated 37,000 rebels and those sheltering with them were beheaded. The ruins of 原城 (Hara-jō) were burned to the ground, then buried — along with the bodies of all the dead — so thoroughly that the site vanished from view.

松倉勝家 (Matsukura Katsuie), the daimyō whose cruelty had ignited the rebellion, was himself executed by the shogunate. He was the only daimyō put to death by the Edo government during the entire period — a sign that even the Tokugawa recognized who was most responsible.

The conclusions the shogunate drew were immediate and lasting. Christianity had organized the rebellion; therefore Christianity must be destroyed. Portuguese traders were expelled in 1639. The remaining foreign presence was confined to the Dutch on the artificial island of 出島 (Dejima) in Nagasaki harbor — the same Dutch who had tried, and failed, to bombard the rebels into submission. Japan's doors closed. They would not open again for more than two hundred years.