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Exile and death

The causes of John's exile are not clear, though Jennifer Barry suggests that they have to do with his connections to Arianism. Other historians, including Wendy Mayer and Geoffrey Dunn, have argued that "the surplus of evidence reveals a struggle between Johannite and anti-Johannite camps in Constantinople soon after John's departure and for a few years after his death". Faced with exile, John Chrysostom wrote an appeal for help to three churchmen: Pope Innocent I; Venerius, the bishop of Mediolanum (Milan); and Chromatius, the bishop of Aquileia. In 1872, church historian William Stephens wrote:

The Patriarch of the Eastern Rome appeals to the great bishops of the West, as the champions of an ecclesiastical discipline which he confesses himself unable to enforce, or to see any prospect of establishing. No jealousy is entertained of the Patriarch of the Old Rome by the patriarch of the New Rome. The interference of Innocent is courted, a certain primacy is accorded him, but at the same time he is not addressed as a supreme arbitrator; assistance and sympathy are solicited from him as from an elder brother, and two other prelates of Italy are joint recipients with him of the appeal.

Pope Innocent I protested John's banishment from Constantinople to the town of Cucusus (Göksun) in Cappadocia, but to no avail. Innocent sent a delegation to intercede on behalf of John in 405. It was led by Gaudentius of Brescia; Gaudentius and his companions, two bishops, encountered many difficulties and never reached their goal of entering Constantinople.

John wrote letters which still held great influence in Constantinople. As a result of this, he was further exiled from Cucusus (where he stayed from 404 to 407) to Pitiunt (Pityus) (in modern Georgia). He never reached this destination alive, as he died at Comana Pontica (modern-day Gümenek, Tokat, Turkey) on 14 September 407 during the journey. He died in the Presbyterium or community of the clergy belonging to the church of Saint Basiliscus of Comana. His last words are said to have been " Δόξα τῷ Θεῷ πάντων ἕνεκεν " ('Glory be to God for all things').