During the establishment of the Independent State of Croatia, Mušicki remained with the Yugoslavian army and was taken prisoner by Croatian forces. However, he was soon released and sent to Belgrade where he came into contact with ZBOR leader Dimitrije Ljotić. He was later made commander of the newly formed Serbian Volunteer Corps set up by Milan Nedić's government. He served in this post for much of the war. His final act as commander of the corps was to make his troops part of the Yugoslav Army in the Fatherland (more commonly known as Chetniks). This was done near the war's end to save what was left of pre-World War II Kingdom of Yugoslavia after it became clear that the Anglo-American Alliance favoured the Communists to take over the country.
On August 24, 1945 he was caught by the British Army and was later handed over to officials from communist Yugoslavia. Mušicki was accused along with Draža Mihailović. He was sentenced for several crimes, including responsibility for the Kragujevac massacre and Axis-collaboration. He was executed in Belgrade in 1946.