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Archbishop Vitaly's mentoring culminating in the question of the EOCC's canonicity, which prompted Toombs and his second wife Maryangela to be tonsured monastics at [[Holy Trinity Monastery (Jordanville, New York)|Holy Trinity Monastery]] in Jordanville, New York in early July of 1951. A few days later Fr. James (Toombs) was consecrated on the [[feast day|Feast]] of the Holy [[Apostles]] [[Apostle Peter|Peter]] and [[Apostle Paul|Paul]] on July 21 as the Bishop of Manhattan in vicar the Diocese of Eastern America and Jersey City at the [[New Kursk-Root Hermitage (Mahopac, New York)|New Kursk-Root Hermitage]] in Mahopac, New York. Concelebrating with Metropolitan Anastasy were Archbishop Vitaly, Archbishop [[John (Maximovitch) the Wonderworker|John (Maximovich) of Paris]], Bishop [[Nikon (Rklitski) of Florida|Nikon (Rklitzky) of Florida]], and Bishop [[Seraphim (Ivanov) of Chicago|Seraphim (Ivanov) of Holy Trinity]]. Archbishop James was installed at as the first Bishop Archbishop of Manhattan and was tasked with heading a completely autonomous American Orthodox Mission within ROCOR, insofar that he was allowed by the Synod to stay short-haired and clean-shaven to adequately perform his duty. In 1953, Bishop James single-handedly changed the practice of receiving [[Roman Catholic|Roman Catholics]] into the [[Russian Orthodox Church]] when he delivered a report stating that the American Orthodox Mission received all [[convert|converts]] by [[baptism]], where prior to the Russian Revolution, Catholic converts were accepted simply through [[confession]]. The change garnered no opposition.

Upon his entry into ROCOR, Gregory and John Adair engaged Bishop Archbishop James in a lawsuit over the Cathedral of Our Saviour on West 69th Street. Fearing that he would take the church with him, the Adair Brothers claimed rather that it was property of the Eastern Orthodox Catholic Church. There is speculation that a canon lawyer from the North American Metropolia came to the EOCC's aid and helped them win rights to the church in 1952, which was later sold for a great sum to make way for Lincoln Center. For the remainder of his life, Bishop Archbishop James would serve in the Chapel of the Holy Apostles, built into his apartment.

Though not part of the Synod of Bishops, during his tenure in ROCOR, Bishop Archbishop James was very active. He was a concelebrant at the consecration of Bishop [[Averky (Taushev) of Syracuse]] on the [[Pentecost#After Pentecost|Feast of the Holy Spirit]] in 1953 alongside Metropolitan Anastasy and others, attended Hierarchical Council meetings and celebrations at Holy Trinity Monastery and New Kurk-Root Hermitage, and in so doing, meeting most of the Synod of Bishops. Bishop Archishop James's attained a flock, but the language barrier between American and Émigré made much of anything outside the Mission difficult. Those who wished to study at [[Holy Trinity Orthodox Seminary (Jordanville, New York)|Holy Trinity Seminary]] in Jordanville could only be instructed by Archpriest [[Andrei (Rymarenko) of Rockland|Adrian Rymarenko]], with Archimandrite [[Lazarus (Moore)]] helping translate seminary materials. Bishop Archbishop James's former wife Maryangela couldn't join the Russian-speaking [[Holy Dormition Convent (Nanuet, New York)|Holy Dormition Convent]] "Novo-Diveevo" in Nanuet, New York, and so was allowed to live separately on the second floor of his apartment.

However, his episcopacy was not without controversy. Bishop Archbishop James's past connections with the esoteric masonic Christianity of George Winslow Plummer, reminiscent of the Theosophy movement which raged in Pre-Revolutionary Russia, and association with wayward and wandering bishops led to rumors of occultist practices taking place within the Mission. Another sore point came with the inconvenient living arrangement of the formerly-married bishop and nun. Furthermore, to many of the Russian émigré mindset, English-language translations of services were seen as very taboo, compounded by the seeming isolationism of the American Orthodox Mission. [[Protopresbyter]] [[Gregory (Grabbe) of Washington|George Grabbe]] led the opposition against Bishop Archbishop James, drawing several members of the Synod of Bishops to his side. By 1955, Bishop Archbishop James expressed his desire to Metropolitan Anastasy to continue missionary work as hierarch of an independent American Church.