In 1570/1571 Godunov strengthened his position at court by his marriage to Maria Grigorievna Skuratova-Belskaya, the daughter of Ivan's abominable favorite Malyuta Skuratov-Belskiy. In 1580 the Tsar chose Irina (Alexandra) Feodorovna Godunova (1557 – October 26/November 23, 1603), the sister of Godunov, to be the wife of his son and heir, the fourteen year old Tsarevich Feodor Ivanovich (1557–1598); on this occasion Godunov was promoted to the rank of Boyar. On November 15, 1581, Godunov was present on the scene of Ivans murder of his own son, also called Ivan. Though he tried to intervene, he received blows from the Tsars sceptre. Ivan immediately repented, and Godunov rushed to get help for the dying Tsarevich, who died four days later.
On his deathbed Ivan appointed a council consisting of Godunov, Feodor Nikitich Romanov, and Vasili Shuiski along with others, to guide his son and successor; for Feodor was feeble both in mind and in health; “he took refuge from the dangers of the palace in devotion to religion; and though his people called him a saint, they recognized that he lacked the iron to govern men.”
Upon his death Ivan also left behind the three year old Dmitri Ivanovich (1581–1591), born from his seventh and last marriage. As the Orthodox Church recognized only the initial three marriages, and any offspring thereof, as legitimate, Dmitri (and his mother's family) technically had no real claim to the throne.
Still, taking no chances, the Council, shortly after Ivan's death, had both Dmitri and his mother Maria Nagaya moved to Uglich some 120 miles north of Moscow. It was there that Dmitri died a few years later at the age of ten (1591). An official commission, headed by Vasili Shuiski, was sent to determine the cause of death; the official verdict was that the boy had cut his throat during an epileptic seizure. Ivan's widow claimed that her son had been murdered by Godunov's agents. Godunov's guilt was never established and shortly thereafter Dmitri's mother was forced to take the veil. As for Dmitri Ivanovich he was laid to rest and promptly, though temporarily, forgotten.
A conspiracy against him of all the other great boyars and the metropolitan Dionysius, which sought to break Boris's power by divorcing the Tsar from Godunov's childless sister, only ended in the banishment or tonsuring of the malcontents. Henceforth Godunov was omnipotent. The direction of affairs passed entirely into his hands, and he corresponded with foreign princes as their equal.
His policy was generally pacific, but always most prudent. In 1595 he recovered from Sweden the towns lost during the former reign. Five years previously he had defeated a Tatar raid upon Moscow, for which service he received the title of Konyushy (or in 1584), an obsolete dignity even higher than that of Boyar. Towards Turkey he maintained an independent attitude, supporting an anti-Turkish faction in the Crimea, and furnishing the emperor with subsidies in his war against the sultan.
Godunov encouraged English merchants to trade with Russia by exempting them from tolls. He civilized the north-eastern and south-eastern borders of Russia by building numerous towns and fortresses to keep the Tatar and Finnic tribes in order. These towns included Samara, Saratov, Voronezh, Tsaritsyn, and a whole series of lesser towns. He also re-colonized Siberia, which had been slipping from the grasp of Russia, and formed scores of new settlements, including Tobolsk and other large centres.
It was during his government that the Russian Orthodox Church received its patriarchate, which placed it on an equal footing with the ancient Eastern churches and emancipated it from the influence of the Patriarch of Constantinople. This reform was meant to please the ruling monarch, as Feodor took extraordinary interest in church affairs.
Boris's most important domestic reform was the 1587 decree forbidding the peasantry to transfer themselves from one landowner to another, thus binding them to the soil. The object of this ordinance was to secure revenue, but it led to the institution of serfdom in its most grinding form.
During the first years of his reign he was both popular and prosperous, and ruled excellently. He fully recognized the need for Russia to catch up to the intellectual progress of the West, and did his utmost to bring about educational and social reforms. He was the first tsar to import foreign teachers on a great scale, the first to send young Russians abroad to be educated, the first to allow Lutheran churches to be built in Russia. Having won the Russo–Swedish War (1590–1595), he felt the necessity of a Baltic seaboard, and attempted to obtain Livonia by diplomatic means. He cultivated friendly relations with the Scandinavians, in order to intermarry if possible with foreign royal houses, so as to increase the dignity of his own dynasty.
Undoubtedly Boris was one of the greatest of the Russian tsars. But his great qualities were overshadowed by an incurable suspiciousness, which made it impossible for him to act cordially with those about him. His fear of possible pretenders induced him to go so far as to forbid the greatest of the boyars to marry. He also encouraged informers and persecuted suspects on their unsupported statements. The Romanov family especially suffered severely from this behaviour. He also declined the personal union proposed to him in 1600 by the diplomatic mission led by Lew Sapieha from the Polish-Lithuanian Commonwealth. Boris died after a lengthy illness and a stroke on April 13/23, 1605, leaving one son, Feodor II, who succeeded him for a few months and then was murdered by the enemies of the Godunovs as was his widow, both murdered in Moscow on June 10/July 20, 1605. Their first son Ivan was born in 1587 and died in 1588, and their daughter Xenia, born in 1582/1591, was engaged to Johann of Schleswig-Holstein, born on July 9, 1583 but he died shortly before announced marriage on October 28, 1602) and she died unmarried and without issue on May 30, 1622 and was buried at St. Trinity Monastery.