Dueñas was ostensibly arrested on suspicion of having knowledge of Tweed's whereabouts. But the priest had been a target of the Japanese since the beginning. Father Dueñas was quite open about his dislike for the Japanese, including two Japanese priests who were sent to Guam during the war - not by Rome - but by the Japanese government. The bishop at the time, Miguel Angel Olano, made Father Dueñas temporary head of the Church on Guam while Olano was in Japan and elsewhere because the Japanese deported all foreign missionaries from Guam. Father Dueñas made it clear that he was the church authority on Guam; no one else. The Japanese priests were Dominic Fukahori and Petro Komatsu. After the war, Fukahori became bishop of Fukuoka.
Father Dueñas also ruffled the feathers of the Japanese with little acts of defiance. He was even threatened with exile to Rota. When the Japanese knew that the American invasion was imminent, they were in the mood to take others down with them, including Father Dueñas.
The exact location of his remains were unknown until 1945 when Father Oscar L. Calvo got a Saipanese interpreter who had been at the beheading to take him to the site in Tå'i. The spot was dug up, Father Dueñas' remains were identified by clothing and other personal effects, and his remains were brought to Inarajan were they now rest in the floor of the church sanctuary.
Father Dueñas was the second Chamorro to be ordained a Catholic priest; Father Jose Palomo was the first. He had been a priest for only 6 years when the Japanese beheaded him, and he was only 33 years old.