This state of affairs changed with the murder of Photius' patron [[Bardas]] in 866 and of the Emperor Michael in 867 by his colleague [[Basil I the Macedonian|Basil the Macedonian]], who now usurped the throne. Photius was deposed as [[patriarch]] not so much because he was a protegé of Bardas and Michael, but because Basil I was seeking an alliance with the pope and the western emperor. Photius was removed from his office and banished around the end of September 867, and Ignatius was reinstated on [[November 23]]. During his second patriarchate, Ignatius followed a policy not very different from that of Photius. This perhaps helped improve relations between the two, and circa 876 Photius was suddenly recalled to Constantinople and entrusted with the education of the emperor's children, becoming an advisor to Ignatius. On the death of Ignatius in October 877, Photius, after the requisite show of reluctance, having been recommended by Ignatius prior to his death, was restored to the patriarchal throne.
Photius now obtained the formal recognition of the Christian world in a council convened at Constantinople in November 879. The legates of [[Pope John VIII]] attended, prepared to acknowledge Photius as legitimate patriarch, a concession for which the pope was much censured by Latin opinion. The patriarch stood firm on the main points contested between the eastern and western Churches, the demanded apology to the pope, the ecclesiastical jurisdiction over [[Bulgaria]], and the introduction of the [[filioque
clause]] into the [[Nicene creed|creed]]. Eventually Photius refused to apologize or accept the ''filioque'', and the papal legates made do with his return of Bulgaria to Rome. This concession, however, was purely nominal, as Bulgaria's return to the [[Byzantine rite]] in 870 had already made it an [[autocephalous]] church. Without the consent of [[Boris I of Bulgaria]], the papacy was unable to enforce its claims.
During the altercations between Basil I and his heir [[Leo VI the Wise|Leo VI]], Photius took the side of the emperor. Consequently, when Basil died in 886 and Leo became senior emperor, Photius was dismissed and banished, although he had been Leo's tutor. Photius was sent into exile to the [[monastery]] of Bordi in [[Armenia]]. From this time Photius disappears from history. No letters of this period of his life are extant. The precise date of his death is not known, but it is said to have occurred on [[February 6]], 893.