Удалиться с патриаршего престола Никон решил не вдруг. Поначалу, как стал он высшим российским архиереем, царь и бояре по их клятвенному обещанию слушать его во всем служили Христовой церкви праведно. Был молодой Алексей Михайлович кроток и послушлив, так что, когда по прошествии трех лет Никон просил отпустить его с патриаршества, самодержец сильно уговаривал остаться, не зная, как без него Церковь управить. Никон снизошел к сей просьбе и пуще прежнего стал обличать сановников и народ за небрежение церковным чином и мирские безобразия, а также и самого царя евангельским и апостольским заповедям учить.

С годами, однако, стал Алексей Михайлович все больше тяготиться суровыми Никона требованиями, почувствовал для власти своей тесноту, начал многие дела по своей воле вершить и по совету с боярами. Царское правительство стало более последовательно соблюдать Соборное уложение о светском суде над священным чином, вынуждено было в условиях тяжелой войны пополнять казну за счет церковных и монастырских доходов, а главное — сам Алексей Михайлович во многих случаях Никона патриарха перестал слушать, начал даже укорять! Этого унижения священства перед царством патриарх не мог ни спустить, ни перенести. Самолюбие обоих владык страдало.

Прямая распря случилась 6 июля 1658 г. Во дворце самодержца давали пир в честь приехавшего из Грузии царевича Теймураза. Патриарх, вопреки обычаю, не был приглашен. Он был взбешен и отправил в царский дворец своего стряпчего Дмитрия Мещерского, князя известной фамилии. На беду, перед дворцом собралась огромная толпа поглазеть на церемониальное шествие. Окольничий Богдан Матвеевич Хитрово, отвечавший за порядок прибытия гостей, рассвирепел, расчищая путь, настолько, что среди народа трахнул палкой по голове и Мещерского.

— Напрасно ты бьешь меня, Богдан Матвеевич, — крикнул князь, — я здесь не просто, но с делом!

— Да кто ты есть?! — осведомился осерчавший распорядитель шествия, который, как и многие придворные, был глубоко оскорблен многолетним вмешательством духовенства в государственные дела.

— Я патриарший человек, — отвечал Мещерский, — и с делом прислан.

— Ах ты… — сказал Хитрово, хватив князя палкой по лбу со всей силы, нанеся основательную рану. — Не дорожись–де патриархом!

As soon as Meshchersky, supported by the arms of some people, reached the patriarchal palace and told how the matter had been, Nikon wrote a harsh letter to Alexei Mikhailovich, demanding that he immediately give satisfaction for the offense of his solicitor. The influence of the patriarch and the general fear of him were so great that his message was handed to the tsar right at the banquet table. The Tsar immediately dictated a reply message that he would investigate this matter himself and personally see Nikon.

The tsar's stolnik Matyushin brought this answer to the Patriarch, but Nikon was too furious to wait. He sent the stolnik back, wanting an immediate investigation. Alexei Mikhailovich was still sitting at the table with the Tsarevich and the boyars, but he found time to send Nikon another soothing letter. Having read it, the patriarch said to the tsar's stolnik with a threat: "The great sovereign is free not to give me defense, but I will manage the Church with him!"

However, in vain did Nikon prepare a harsh sermon to the autocrat who had lost his grip. The Tsar did not want to listen to lectures any longer, and the boyars were quite tired of Nikon's six-year rule: they unanimously dissuaded Alexei Mikhailovich from meeting with the Patriarch. Nikon did not go to the palace – Alexei Mikhailovich and his court did not appear at the solemn patriarchal service on July 8, the feast of the Kazan Mother of God, which was usually attended.

Nikon still hoped to humble the tsar and on July 10, on the feast of the Lord's Robe (sent to Tsar Mikhail Fyodorovich by the Persian shah), he ordered the annunciation to be ringed at the large bells until Alexei Mikhailovich appeared at the Assumption Cathedral. He forgot how the Tsar had neglected the services of Patriarch Joseph, praying with him, Nikon, in the palace churches, and was sure that piety would force the autocrat to overcome his pride.

For a long time, large bells rang in the Kremlin, calling first to vespers, and then to all-night vigil. Nikon was confused. His power as a great bishop, placed by God Himself above that of the tsar, dissolved like smoke. The crowds that had been gathering at the entrance to the patriarchal palace since early morning disappeared. Boyars and clerks did not appear with reports. Foreign bishops did not come in to talk. Metropolitans and archbishops, archimandrites and abbots, who were always afraid of his wrath, hid somewhere. Even the poor priests, who dragged their pitiful bribes to the patriarchal clerks for putting them in their place or changing the parish, fled around Moscow, waiting to see how the quarrel "at the top" would end.

The Patriarch suddenly discovered that his consecrated power was almost entirely the power of the tsar's favorite. True, the enormous wealth of the Church ensured his influence, but not so obvious and tangible as he was accustomed to. The somny of the clergy would not have helped him in the conflict with the autocrat, on whom the overwhelming majority, if not all, of them pinned their hopes in the matter of defending the Church and piety. Nikon could not even change the bishops without the permission of the tsar, let alone punish them: the patriarchal clerks instantly remembered that the lawful trial of the clergy belonged to the Monastic Prikaz.

Seeing that he was left alone and had nothing to do with – the royal power took over the court and all ecclesiastical administration – Nikon gave room to anger. And then, after matins, Prince Grigory Romodanovsky came to the Dormition Cathedral and said: "The Tsar's Majesty is angry with you, and for this reason he did not come to matins, and did not command himself to be expected at the Holy Liturgy." And Romodanovsky also said: "You have neglected the Tsar's Majesty and are called a great sovereign, but we have only one great sovereign – the Tsar."