Since all previous assistants sent to Japan to help Abp. Nicholas returned to Russia, the latter asked Sergius if he intended to remain in Japan permanently or to return in a few years as those earlier had. Sergius affirmed that he had come dedicating himself to remain for the rest of his life. Over the next few years Sergius involved himself deeply in the church and mission and gradually assumed management of the organization, allowing Nicholas to devote his time to the seminary and his extensive translation work. Sergius engrossed himself particularly in missionary efforts, visiting widely, from the southern part of Sakhalin that Japan had gained from Russia after the Russo-Japanese war, to Kuril Islands and Manchuria.

Within some six years, however, Sergius had to contend with a different and difficult world. With the Russian Revolution of 1917 and the subsequent takeover by the Bolsheviks, funding for the Japanese mission was cut off. Although this meant that the archbishop had to cut the activities of the mission severely, it nonetheless survived.