During Operation Kraai (the second Dutch military aggression against Indonesia), Yogyakarta was captured and the Indonesian leaders including Sukarno and Hatta were seized and exiled to Bangka. Ratulangi was seized by the Dutch on 25 December 1948. He was transferred to Jakarta on 12 January 1949 to be subsequently transferred to Bangka. However, due to his failing health, he was allowed to stay in Jakarta on house arrest. Ratulangi died on 30 June 1949. Ratulangi was temporarily buried in Tanah Abang, Jakarta. On 23 July 1949, his remains were transported to Manado on the KPM ship "Swartenhondt". On 1 August 1949, the ship reached Manado. The next day Ratulangi's remains were transported and buried in his hometown of Tondano.