The pressure exerted by the Shimazu stepped up a notch in the aftermath of the agreement for assistance from Hideyoshi. Shimazu Yoshihisa moved north, establishing a camp at Higo Yatsushiro (肥後八代), while Shimazu Tadanaga (Yoshihisa`s adopted sibling) and Ijūin Tadamune (伊集院忠棟) swung by Kōrazan to put pressure on Chikuzen and Chikugo provinces. Secret messages were passed from the Shimazu to prominent regional lords in Bungo, a tactic of subterfuge that produced results, the most surprising of which was the defection to the Shimazu of Sōrin`s second son and heir to the Tahara family, Tahara Chikaie. This defection was to prove particularly useful to the Shimazu in their eventual invasion of Bungo. Upon discovering Chikaie`s betrayal, Yoshimune vented his fury by banishing Chikaie and even attempted to have him killed. Only the intervention of Sōrin in between both parties diffused the situation and allowed Chikaie to escape with his life.(270-271)

In the meantime, Yoshimune continued his calls for assistance from Hideyoshi. Finally, in the 3rd month of Tenshō 15 (1587), Hideyoshi decided to launch his campaign to subjugate Kyushu. He had the father and son rulers of Tosa province, Chosokabe Motochika and Nobuchika, sent as an advance guard to Bungo, while Mōri Terumoto, Kitsukawa Motoharu, and Kobayakawa Takakage of Chūgoku were ordered to advance into Buzen. Two direct retainers of Hideyoshi, Sengoku Hidehisa (仙石秀久) of Sanuki province and the Christian daimyō Kodera Kanbe`ei (小寺官兵衛, later known as Kuroda Yoshitaka and by the Buddhist name of Josui) were ordered to act as observers of the Chūgoku and Shikoku armies, and so they too made their way to Bungo and Buzen.(271)

Shimazu Yoshihisa, fearing that Bungo might slip from his grasp, led a large army from Higo into Hyuga. There he split the army in half. In the 11th month of Tenshō 14 (1586), with part of the Shimazu army under the command of Yoshihisa`s younger brother Yoshihiro in Higo and the other half camped on the Hyuga/Bungo border under the command of Shimazu Iehisa, Yoshihisa ordered both armies to invade Bungo. The strategy of sending messages in secret to retainers of the Ōtomo that resided in the southern regions of Ōno and Naoiri gun proved worthwhile for the Shimazu. First Betsugi Shigesumi (lord of Yoridake castle), Ichimada Sōai (一万田宗挨, lord of Torii castle), and Shibata Shōan (柴田紹安, lord of Asahidake castle) in Ōno gun, and Shiga Dōun (lord of Shirani castle), Shiga Dōeki, Kutami Sōreki (lord of Yamano castle) and Nyūta Sōwa (入田宗和) in Naoiri gun all defected to the Shimazu and acted in unison with the invading armies. It was now blatantly clear just how weak the Ōtomo`s grip on their retainers had become.(272)

Iehisa`s army, after exiting from the Azusa pass (梓峠), rapidly advanced north, capturing all the castles in Ogata shōen and Notsuin as far as Ōno Matsuozan. One part of this army then broke off from the main force and moved east into Kaifu gun. It lay siege to Saiki Koretada (佐伯惟定) at Saiki Togamure castle (栂牟礼). However it was unable to achieve its objective and so retreated. In the meantime, in the 12th month the main Shimazu army (under Iehisa) arrived at the foot of Sōrin`s castle at Usuki. Part of this army then moved off to the west to lay siege to Toshimitsu Sōgyo (利光宗魚) at Tsuruga castle in Oita gun, eventually capturing the castle. This prompted Yoshimune, Sengoku Hidehisa, and Chosokabe Motochika to advance towards the Shimazu from Funai in order to provide reinforcements to the army besieged at Usuki. However their move was checked by Iehisa, who inflicted a major defeat on the allied army at the battle of Betsugigawa (戸次川の戦い). This battle saw the death of Chosokabe Nobuchika and the retreat of Yoshimune to the west - first to the castle of Takazaki, and then to the castle of Ryūō. For his part, Hidehisa fled to Buzen Kokura castle, while Motochika retreated as far as Hiburishima (日振島) in Iyo province. As it appeared that Yoshimune had essentially forsaken Bungo, his retreat earned the ire of Hideyoshi, and is cited as one of the reasons behind the dismissal of Yoshimune in later years.(272) The Jesuits in turn lay the principal blame for the defeat in the incompetence displayed by Yoshimune and Hidehisa, reasons which have generally been regarded as valid.(272) 

While these events were unfolding, Yoshihiro`s army invaded Bungo from Higo with Niiro Tadamoto (新納忠元) in the vanguard. After passing Naminogahara (波野原), the army halted in order to lay siege to Shiga Chikayoshi (志賀親次) at Oka castle. At the time, Chikayoshi was the only local ruler within Bungo to successfully resist a direct attack from the Shimazu. Chikayoshi requested aid from Yoshimune, yet Yoshimune was in no position to be able to give his support. Instead, Yoshimune intended to wage a guerrilla war against Yoshihiro`s army, harrying and harassing them at every turn. In the end, Yoshihiro called off the siege in order to concentrate on advancing into Ōita gun. In the first month of Tenshō 15 (1587), Yoshihiro`s army lay siege to Yufuin and the castle of Tsunomure (角牟礼) in Kusu gun.(274)

While this was occuring, Iehisa`s army entered a recently vacated Funai before once again making its way towards the eastern coast in order to lay siege to Usuki castle. Upon entering Usuki territory, Iehisa`s army spent three days forming a siege ring around the castle. The chapel that Sōrin had built within the town was burned down along with adjoining buildings, and everywhere crucifixes were torn down – all acts that eventually reduced the town of Usuki to rubble. However, as for Usuki castle itself, a large cannon dubbed `kunikuzushi` (国崩, or `destroyer of provinces`) was placed on Sōrin`s orders above the second gate. The firepower demonstrated by this cannon was enough to cause the Shimazu some consternation. Yet as revealed earlier, there were very few warriors within Usuki castle, for the castle was mostly filled with poor mothers and children, leaving it virtually undefended. Moreover, Sōrin didn`t concern himself much with military preparations or issuing orders, instead devoting his time to providing aid to the commoners trapped within the castle and distributing clothing and gruel among the poor.(274)

Yoshimune, upon hearing that Usuki castle was under attack, quickly made his way back to Funai. However he was woefully unprepared to meet the Shimazu in battle for he had fewer men than the Shimazu, and was unable to come up with any stratagem to oppose the Satsuma armies` presence in Bungo. Nevertheless, the Shimazu did suffer their own setback after failing to capture Usuki castle. As discussed earlier, Usuki castle possessed formidable natural defences. This, combined with a fear of attack by a large army advancing from Funai, convinced the Shimazu to lift their siege and withdraw. However as Sōrin had been confined to Usuki castle for the duration of the siege, he believed his territories to be lost, and so sent letters to the missionaries stationed at the Noviciado within the grounds of Usuki castle and the Collegio in Funai, recommending that the missionaries gather up their wealth and flee to the safety of Yamaguchi. Sōrin vowed to remain where he was, joined by a solitary missionary, two acolytes, and a number of townspeople from Usuki. The priest Gomez was ordered to convey the content of Sōrin`s thoughts from Usuki to Funai, a task that came with a considerable amount of risk.(275-276)

Bungo had been plunged into chaos, anarchy reigned, and the roads and sea lanes had become the preserve of bandits and pirates. With sea travel ruled out of the question, it was proving exceedingly difficult to gather all of the missionaries of Funai at Usuki. Meanwhile, many of the residents of Funai chose to flee to other parts of the province, taking their wealth with them. Such was the seriousness of the situation that Yoshimune and Hidehisa were forced to issue an edict banning townspeople from leaving Funai, with the threat of execution for any who tried to defy the ban. Indeed, things had grown dire enough to prompt Padre Gomez to write a letter to Luis Frois at Shimonoseki, who in turn relayed the message on to Kodera Kanbe`ei (小寺官兵衛). In this message, Gomez recommended transferring all of the missionaries` funds to Yamaguchi in addition to transporting the missionaries themselves to safety in Suo. A number of vessels would need to be prepared in advance for this mission, a point that Gomez left to Luis` discretion. For his part, Luis contacted Kodera Kanbe`ei, who agreed to the mission and ordered his subordinates to prepare vessels. However the winter of 1587 was particularly harsh, with poor winds, and Kodera`s own vessels were shored up in a distant part of the country. Kodera decided to approach a number of captains of vessels moored off Usuki, requesting their help in transporting missionaries and their belongings to Yamaguchi. In response, two large vessels left Shiakujima (塩飽島) and made their way to Usuki, picking up their cargo at a reduced price.(276)

Thirty-three Jesuits and around 65 or so followers boarded both vessels, reducing the number of Christian priests and acolytes within the province to just 13. Those left behind would experience a fair degree of hardship during the coming years.(277)

Both Usuki and Funai had been burned to the ground, a situation that would have been very hard to accept for those still loyal to the Ōtomo. The once mighty Ōtomo family, ruler of six provinces, had been reduced to just one. With the capital of Bungo province destroyed, many expected that the Ōtomo would soon disappear. However, very slowly the number of warriors flocking to Bungo to offer their aid to the Ōtomo began to increase, in part encouraged by a rumour that Hideyoshi himself would soon arrive in Kyushu. This rumour reached the Shimazu camp, who thought it wise to retreat in good order. And so in the 3rd month of Tenshō 15 (1587), six months after they had first stepped onto Bungo soil, the Shimazu made the decision to withdraw from Bungo.(277)

In the wake of the withdrawal of the Shimazu, Bungo suffered a virulent epidemic similar in kind to bubonic plague. Countless numbers of commoners died in the absence of any form of medical care. Those missionaries that had chosen to remain in Bungo resided together with Sōrin at his castle in Usuki. However eventually they too would decide to leave. It appears that under the protection of Sōrin, Christianity had flourished within the heart of Bungo, yet the breakup of the system of regional control exercised by the Ōtomo proved to be a large turning point in the fortunes of Christianity.(277)

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