On February 1943, Most Rev. Jose Maria Cuenco, the newly consecrated Bishop came to the Diocese as an Auxiliary of Bishop McCloskey. Many problems demanded his attention and one of them was the Seminary. He had Fr. Eliseo Rodriguez appointed as Rector on May 31, 1943. Then the Bishop and the new Rector tried to resume classes to show the Japanese authorities that the Seminary was a center of learning and to avoid the danger of having the Seminary building occupied for military purposes. However, all their efforts to proved rather, useless. Only two Seminaries, returned to the Seminary, one deacon and one sub-deacon returned to the seminary. They tried again the next year. With the help of the Parish Priests, classes were opened in January 1944 with 23 seminarians major and minor. By the end of March, the Seminarians went home for their summer vacation, but they did not come back nymore. Only five major seminarians were present for the opening of classes on June 15, 9144. One of the seminarians, a deacon, was ordained priest on July. The other four continued their studies up to September 13 when for the first time the American planes started bombing the Mandurriao Airport and one of t bombs lightly damaged the Seminary building. That brought to an end of the Seminary work until January 1946.