structural:reformatting, linguistic:paraphrasing
Political power

From 1652 to 1658, Nikon was not so much the minister as the colleague of the Tsar. Both in public documents and in private letters he was permitted to use the sovereign title. This was especially the case during the wars with the Polish–Lithuanian Commonwealth in 1654–1667, when the tsar was away from Moscow with his armies. In 1654, while starting on his great military campaign, the tsar left Nikon at home as the chief ruler. Needless to say, this created some considerable resentment among the high level boyars.

Nikon made it his mission to remove the Church from secular authority, and permanently separate the Church from the state. He believed that the Church and state should work in harmony, while remaining separate from each other. He stated that "There are two swords of authority, that is, the spiritual and the secular" and that "the supreme Bishop is higher than the Tsar". He also sought to organize the Church with a hierarchy similar to the state's – with the Patriarch in complete control.. On a personal note, Nikon and Aleksei officialized their bond as the Tsar made the Patriarch godfather of all his children.

Nikon especially protested Sobornoye Ulozheniye (Russian Legal Code) of 1649, which reduced the status of the clergy, and made the Church in effect subservient to the state. Also, according to this Code, the taxation of monastery lands was used for the benefit of the state.

But his actions raised up a whole host of enemies against him, and by the summer of 1658 they had convinced Alexius that the sovereign patriarch was eclipsing the sovereign tsar. Alexius suddenly grew cold towards his own "bosom friend," as he called him.