Although the population of native Catholics expanded greatly in the years following his consecration, Soegijapranata was soon faced with numerous trials. The Empire of Japan invaded the Indies beginning in early 1942, and during the ensuing occupation numerous churches were seized and clergymen were arrested or killed. Soegijapranata was able to resist several of these seizures, and spent the rest of the occupation serving the Catholics in his vicariate. After President Sukarno proclaimed the country's independence in August 1945, Semarang was overcome with unrest. Soegijapranata helped broker a ceasefire after a five-day battle between Japanese and Indonesian troops and called for the central government to send someone to deal with the unrest and food shortages in the city. However, these problems continued to grow, and in 1947 Soegijapranata moved his seat to Yogyakarta. For the remainder of the national revolution Soegijapranata worked to promote international recognition of Indonesia's independence. Soon after the Dutch, who had returned in late 1945, recognised the country's independence, Soegijapranata returned to Semarang. During the post-revolution years he wrote extensively against communism and expanded the church; he also served as a mediator between several political factions. He was made an archbishop on 3 January 1961, when Semarang was elevated to an ecclesiastical province. At the time he was in Europe, participating in the first session of the Second Vatican Council. Soegijapranata died in 1963, in Steyl, the Netherlands. His body was flown back to Indonesia, where he was made a national hero and interred at Giri Tunggal Heroes' Cemetery in Semarang.