1598. Boris Godunov has retreated to the Novodievichy Monastery near Moscow. The Streltsy police force a crowd to beg Boris to become Tsar of Russia. The boyar Shchelkalov announces that Boris still refuses the throne and sorrows over Russia’s insoluble misery. A procession of pilgrims prays to God for help. The Streltsy warn the crowd to be at the Kremlin the next morning ready to cheer.
The following day the bells of Moscow herald the coronation of Boris. On a square in the Kremlin, the new tsar, overcome by fear and melancholy, implores God to look kindly on him. He invites the people to a feast. The people cheer.
1603. In the Chudov Monastery, the monk Pimen is writing the last chapter of his history of Russia. The novice Grigori awakens from a nightmare and expresses regret that he hasn’t tasted glory in war and society. He questions Pimen about the dead Tsarevich Dimitri, rightful heir to Boris’s throne. Pimen recounts the events of Dimitri’s murder (the assassins implicated Boris before they died) and remarks that the tsarevich would have been Grigori’s age. Alone, Grigori condemns Boris and decides to escape the cloister.
Now on a mission to expose Boris and proclaim himself the Tsarevich Dimitri, Grigori is trying to cross into Lithuania to find support for his cause. He falls in with two vagrant monks, Varlaam and Missail, at an inn near the border, and uses them as cover. No sooner has he asked directions to the border from the innkeeper, who warns that the frontier is heavily patrolled, than a police officer enters with a warrant for Grigori’s arrest. The officer is illiterate, so Grigori reads the warrant, substituting a description of Varlaam for his own. But Varlaam can read. Grigori escapes, pursued by the Streltsy.
In Boris’s apartments, his daughter mourns the death of her fiancé. Boris comforts her tenderly, talks intimately with his son about inheriting the throne and its responsibilities, then reflects to himself on the crime that gained him the throne and the fears that torment him. Shuisky, a powerful boyar, brings news of a pretender to the Russian throne, supported by the Polish court and the Pope. When Boris learns that the pretender claims to be Dimitri, he is deeply shaken, and Shuisky reassures him again that the real tsarevich was in fact killed. Shuisky leaves and Boris gives way to his terror, imagining that he sees Dimitri’s ghost. Torn by guilt and regret, he prays for forgiveness.
Grigori, who now openly claims to be Dimitri, has made his way to Sandomir Castle in Poland, where he hopes to court and win the powerful Marina Mnishek. Marina intends to win Grigori in order to realize her ambition of ascending the throne of Russia. But the Jesuit Rangoni has his own plan: Marina must seduce Grigori for the glory of the church, and through their union convert Russia to Catholicism. Grigori awaits Marina in the castle garden, receives assurances of Marina’s love from Rangoni, and finally courts Marina. She rejects his protestations of love until she is certain of his determination to become tsar.
Outside the Cathedral of St. Basil in Moscow, starving peasants debate whether Tsarevich Dimitri still lives, as news reaches them that his troops are near. A group of children torment a Holy Fool and steal his last kopek. When Boris and his court come from the cathedral to distribute alms, the Holy Fool asks Boris to kill the children the way he killed Dimitri. Shuisky orders the Holy Fool seized, but Boris instead asks his accuser to pray for him. The Holy Fool refuses to intercede for a murderer. When Boris’s retinue passes and the people disperse, the Holy Fool laments Russia’s dark future.
In the Duma, the council of boyars passes a death sentence on the pretender. Shuisky arrives with an account of Boris’s hallucinations of the murdered tsarevich. Boris suddenly storms in, disoriented and crying out to Dimitri. When he regains his composure Shuisky brings Pimen before the Duma. Pimen tells of a man who was cured of blindness while praying at Dimitri’s grave. Boris breaks down. He sends the boyars away, calling for his son. Naming him heir to his throne, he bids a loving farewell to the boy and dies.
In a forest clearing near Kromy, an angry mob seizes and humiliates several boyars and Streltsy police. Varlaam and Missail enter proclaiming Boris’s guilt. The mob strengthens its resolve to tear down the old order, and when two Jesuits appear, at the vanguard of the Polish-Catholic advance, they are attacked and brutalized by the crowd. The false Dimitri arrives with Marina, Rangoni, and his army. He calls for the cheering people to follow him on his march to Moscow. The Holy Fool stays behind, lamenting Russia’s bleak, uncertain fate.