The Miyako Island survivors came ashore on Taiwan's southeastern coast and moved inland, entering territory controlled by the Paiwan, one of Taiwan's indigenous peoples. They found shelter with a seventy-three-year-old Hakka trader named Deng Tianbao. The Paiwan men found them there. What exactly happened next is recorded differently by different sources, and the reasons for it remain genuinely contested. Fifty-four of the Ryukyuan sailors were killed — some in the initial confrontation, others attempting to escape. Three were captured. Nine managed to hide in Deng Tianbao's home and were not harmed. Those nine eventually reached another Hakka settlement called Poliac, where Deng's son-in-law, Yang Youwang, sheltered them for forty days. Yang arranged the ransom of three of the captives and eventually sent all the survivors safely to Taiwan Prefecture, the colonial administrative center that is now Tainan. From there they traveled to Fuzhou, and in July 1872 they sailed home to Naha.

The causes of the killings have been discussed for more than 150 years and have never been fully resolved. One account, recorded from Lianes Punanang, a Mudan local with Paiwan heritage, describes sixty-six men entering the village of Kuskus without understanding the territory they were crossing. They took food and water — items that, in Paiwan custom, were symbols of protection and peaceful engagement between parties who had formally acknowledged each other. "In Paiwan tribal tradition," Punanang recounted, "drinking water offered by a stranger means agreeing to peaceful engagement between equals. But the abrupt disappearance breached that agreement, turning guests into enemies." Whether the Ryukyuans understood any of this — whether the encounter that preceded the killings was a misread of hospitality, a failure of ransom negotiation, or something else — is not certain. The Paiwan were a sovereign people governing their own territory under their own law. The Ryukyuans were sailors far from home who did not speak the language and had no guide. The deaths were real on all sides of the confusion.

King Shō Tai of the Ryukyu Kingdom did not ask Japan for help. He sent a reward to Chinese officials in Fuzhou for returning his twelve surviving subjects and left it there. The Ryukyu Kingdom was a small, independent state that had managed its relationships carefully for centuries — tributary to both China and, since 1609, to the Satsuma Domain of Japan. Japan, however, was not interested in leaving the matter alone. In October 1872, Japanese officials formally dethroned Shō Tai, unilaterally reclassifying the Ryukyu Kingdom as a Japanese domain. The dead Miyako sailors, who had not been Japanese nationals at the time of their deaths, were retrospectively claimed as "Japanese nationals" whom Japan had an obligation to avenge. The Qing government, when pressed for accountability over the actions of the Paiwan, declined — on the grounds, as they put it, that "civilization had not been extended to the region." That response gave Japan's government the diplomatic opening it wanted.

In May 1874, approximately 3,600 Japanese troops landed on the southern tip of Taiwan. The stated purpose was to punish the Paiwan for the killing of the Ryukyuan sailors. The actual geopolitical purpose was to test the limits of Qing sovereignty over Taiwan and to establish Japan's claim to the Ryukyu Islands. Fighting occurred in the mountains of southern Taiwan, including in Mudan township itself, where the Paiwan defended their territory against a force that held a significant military advantage. Both sides suffered losses; the campaign lasted into the summer and autumn. A diplomatic settlement eventually ended the expedition, with Japan withdrawing from Taiwan in exchange for Qing payment of an indemnity — a payment that implicitly acknowledged Japan's claim over the Ryukyu Islands. The annexation of the Ryukyu Kingdom was completed in 1879. The island group became Okinawa Prefecture. Shō Tai died in Tokyo in 1901, in exile.

Professor Matayoshi Seikiyo, writing about the incident's legacy, argued that it produced two interlocking outcomes: it resolved the question of Ryukyuan sovereignty in Japan's favor, and it served as the first military step toward Japan's eventual colonization of Taiwan in 1895. Both assessments have held up under subsequent historical scrutiny. What is harder to track in the historical record is the human dimension: the fifty-four sailors who left Miyako Island on ordinary business and did not return; the Paiwan people who defended their territory according to their own laws and were afterward subject to a punitive military campaign; the soldiers on both sides who died in the mountains of southern Taiwan in 1874. Reconciliation visits between descendants of the Miyako sailors and descendants of the Paiwan have been taking place since 2004. As Lianes Punanang put it: "On the whole, both my people and our Miyako counterparts were victims, but the sad thing is that their descendants have had to wait for 140 years to be able to talk about what reportedly happened."