[4] Following Straughn's capture and subsequent execution by the Japanese in August 1943, the Marking Guerrillas became an independent force, operating primarily in the Sierra Madre mountains of Luzon 50 km (31 miles) southeast of Manila.

During this time, the guerrillas printed their own banknotes to fund the anti-Japanese resistance and be used as currency for local Filipino communities that they had freed from Japanese control.

[6] Units of the Marking Guerrillas participated in the Battle of Manila, where they were responsible for the capture of Japanese collaborator and former Philippine president Emilio Aguinaldo, whose home they raided on February 8, 1945.

According to Aguinaldo, the guerrillas stole and destroyed many of his belongings during the raid, including jewelry, articles of clothing, documents, and tens of thousands worth of pesos and yen, and had also assaulted his niece.

"[10] The Marking Guerrillas ceased operations and disbanded shortly after their victory at the Ipo Dam, largely due to the departure of Yay Panlilio to the United States in early April of 1945.