[1][2] Due to ongoing instability in Borneo, as well as open conflict with the Republican forces in Java and Sumatra, van Mook decided to focus on the Great East, and to organize a conference in order to establish a state in this region.

This was the result of pressure from the Dutch Catholic Party, which wished to continue the missionary activities in the region, although van Mook claimed that financial and ethnic issues were the reason.

[6][7][8] Due to the fact that the request for any Papuan representatives in the conference was rejected by the Dutch authorities, on 12 December 1946, Nicolaas Jouwe, Marthen Indey, and Corinus Krey sent a telegram to van Mook in Denpasar to oppose the formation of the State of East Indonesia as it did not include Western New Guinea.

In his absence, General Government Commissioner van Hoven chaired the opening session and presented a draft legal basis for an independent State of the Great East.

It included the following provisions:[12] On 9 December, conference delegates expressed support for the Linggadjati Agreement as a basis for the establishment of the United States of Indonesia, and called for it to be ratified immediately in cables sent to the Central Indonesian National Committee in Yogyakarta and to the Dutch parliament.

[11][18] After the conference ended, President Soekawati and Prime Minister Designate Nadjamoeddin traveled to Jakarta to hold meetings to establish the first cabinet, which was announced on 13 January 1947.

This criticism intensified when the provisional legislature held its first session in Makassar, at which many Dutch-appointed delegates expressed support for the Indonesian Republic rather than the Dutch plans for the federal state.

Marthen Indey (as deputy leader of the party) managed to travel to Ambon on 7 January 1947 to meet with pro-Indonesian Moluccan figures, but he was caught by Dutch authorities on 23 March 1947 and later transferred to Hollandia from Biak and sentenced to 4 years in prison.