At the time of Raffles ruled Java replaced Janssens, Sultanate Yogyakarta threatened dibubarkan.Campur Mangkunegaran hands with Legion Mangkunegaran successfulto prevent the dissolution of the Sultanate with the completion of the founding of the Duchy Paku Alaman.
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In the two periods of the Governor-General (Daendels and Raffles), Yogyakarta suppressed with military force to compel Hamengkubuwono II down tahta.Di December 1810 Daendels with troops 4200 soldiers stormed Yogyakarta.Daendels reduce Hamengkubuwono II and then raised the son of the Crown of Yogyakarta as Hamengkubuwono III and returned to Batavia with the Prince Natakusuma as tawanan.Pada month replacement in July 1812 with 2,000 soldiers stormed the Raffles Yogyakarta.