After the atomic bombings of Hiroshima and Nagasaki and the proclamation of Indonesian independence in August 1945, the Japanese began withdrawing from the country.
In support of the new Republic, Soegijapranata had an Indonesian flag flown in front of the Gedangan Rectory; however, he did not formally recognise the nation's independence, owing to his correspondence with Willekens regarding the Church's neutrality.
He and his clergy treated injured Dutch missionaries, who had recently been released from internment, at the rectory.
The Dutch clergy were malnourished, and several required treatment at a hospital.
Some were later taken to Indonesian-run internment camps, but the Catholics were still allowed to look after them.
Meanwhile, inter-religious strife led to the burning of several mission buildings and the murder of some clergymen.
The government also took several buildings, and some that had been seized by the Japanese were not returned.

Allied forces sent to disarm the Japanese and repatriate prisoners of war arrived in Indonesia in September 1945.
In Semarang, this led to a conflict between Japanese forces and Indonesian rebels, that began on 15 October; the Indonesians aimed to confiscate the Japanese weapons.
Allied forces began landing in the city on 20 October 1945; a small group was sent to Gedangan to speak with Soegijapranata.
Concerned with civilian suffering, the vicar apostolic told the Allies that they must stop the battle; the Allies could not comply as they did not know the Japanese commander.
Soegijapranata then contacted the Japanese and, that afternoon, brokered a cease-fire agreement in his office at Gedangan, despite Indonesian forces' firing at the Gurkha soldiers posted in front of the building.

Military conflicts throughout the area and an ongoing Allied presence led to food shortages throughout the city, as well as constant blackouts and the establishment of a curfew.
Civilian-run groups attempted to deal with the food shortages but were unable to cope.
In an attempt to deal with these issues, Soegijapranata sent a local man, Dwidjosewojo, to the capital at Jakarta – renamed from Batavia during the Japanese occupation – to speak with the central government.
Dwidjosewojo met with Prime Minister Sutan Sjahrir, who sent Wongsonegoro to help establish a civilian government, installing Moch.
Ikhsan as mayor.
The city's government was, however, still unable to handle the crisis, and the major figures in this government were later captured by the Dutch-run Netherlands-Indies Civil Administration (Nederlandsch Indië Civil Administratie, or NICA) and imprisoned; Soegijapranata, although he at times harboured Indonesian revolutionaries, was spared.

In January 1946 the Indonesian government moved from Jakarta – by then under Dutch control – to Yogyakarta.
This was followed by a widespread exodus of civilians fleeing the advancing NICA soldiers.
Soegijapranata at first stayed in Semarang, working to establish patrols and watches.
He also corresponded with Willekens in Jakarta, although the elder bishop considered the revolution an internal security matter for the Dutch and not an issue for the Church.
However, in early 1947 Soegijapranata moved to Yogyakarta, allowing easy communication with the political leadership.
He established his seat at St Yoseph in Bintaran and counselled young Catholics to fight for their country, saying that they should only return "once they were dead".
Soegijapranata was present during several battles that arose where he was preaching.

After the Linggadjati Agreement failed to solve conflicts between Indonesia and the Netherlands and the Dutch attacked republicans on 21 July 1947, Soegijapranata declared that Indonesia's Catholics would work with the Indonesians and called for an end to the war in a speech on Radio Republik Indonesia; van Klinken describes the address as "passionate" and considers it to have boosted the Catholic populace's morale.
Soegijapranata wrote extensively to the Holy See.
In response, the Church leadership sent Georges de Jonghe d'Ardoye to Indonesi
After the atomic bombings of Hiroshima and Nagasaki and the proclamation of Indonesian independence in August 1945, the Japanese began withdrawing from the country. In support of the new Republic, Soegijapranata had an Indonesian flag flown in front of the Gedangan Rectory; however, he did not formally recognise the nation's independence, owing to his correspondence with Willekens regarding the Church's neutrality. He and his clergy treated injured Dutch missionaries, who had recently been released from internment, at the rectory. The Dutch clergy were malnourished, and several required treatment at a hospital. Some were later taken to Indonesian-run internment camps, but the Catholics were still allowed to look after them. Meanwhile, inter-religious strife led to the burning of several mission buildings and the murder of some clergymen. The government also took several buildings, and some that had been seized by the Japanese were not returned.
Allied forces sent to disarm the Japanese and repatriate prisoners of war arrived in Indonesia in September 1945. In Semarang, this led to a conflict between Japanese forces and Indonesian rebels, that began on 15 October; the Indonesians aimed to confiscate the Japanese weapons. Allied forces began landing in the city on 20 October 1945; a small group was sent to Gedangan to speak with Soegijapranata. Concerned with civilian suffering, the vicar apostolic told the Allies that they must stop the battle; the Allies could not comply as they did not know the Japanese commander. Soegijapranata then contacted the Japanese and, that afternoon, brokered a cease-fire agreement in his office at Gedangan, despite Indonesian forces' firing at the Gurkha soldiers posted in front of the building.
Military conflicts throughout the area and an ongoing Allied presence led to food shortages throughout the city, as well as constant blackouts and the establishment of a curfew. Civilian-run groups attempted to deal with the food shortages but were unable to cope. In an attempt to deal with these issues, Soegijapranata sent a local man, Dwidjosewojo, to the capital at Jakarta – renamed from Batavia during the Japanese occupation – to speak with the central government. Dwidjosewojo met with Prime Minister Sutan Sjahrir, who sent Wongsonegoro to help establish a civilian government, installing Moch. Ikhsan as mayor. The city's government was, however, still unable to handle the crisis, and the major figures in this government were later captured by the Dutch-run Netherlands-Indies Civil Administration (Nederlandsch Indië Civil Administratie, or NICA) and imprisoned; Soegijapranata, although he at times harboured Indonesian revolutionaries, was spared.
In January 1946 the Indonesian government moved from Jakarta – by then under Dutch control – to Yogyakarta. This was followed by a widespread exodus of civilians fleeing the advancing NICA soldiers. Soegijapranata at first stayed in Semarang, working to establish patrols and watches. He also corresponded with Willekens in Jakarta, although the elder bishop considered the revolution an internal security matter for the Dutch and not an issue for the Church. However, in early 1947 Soegijapranata moved to Yogyakarta, allowing easy communication with the political leadership. He established his seat at St Yoseph in Bintaran and counselled young Catholics to fight for their country, saying that they should only return "once they were dead". Soegijapranata was present during several battles that arose where he was preaching.
After the Linggadjati Agreement failed to solve conflicts between Indonesia and the Netherlands and the Dutch attacked republicans on 21 July 1947, Soegijapranata declared that Indonesia's Catholics would work with the Indonesians and called for an end to the war in a speech on Radio Republik Indonesia; van Klinken describes the address as "passionate" and considers it to have boosted the Catholic populace's morale. Soegijapranata wrote extensively to the Holy See. In response, the Church leadership sent Georges de Jonghe d'Ardoye to Indonesi
Albertus Soegijapranata