The action takes place in Moscow and Zamoskvorechie in the XVII century.
Red Square. Dawn.
Boyar Shalkovity, a protege of the princess Sophia, dictates the denunciation of the princes Khovanskys, planned to take power into their own hands. Strangers appear in the square. With horror they learn about a rough handling with boyars disliked by authorities. Heavy thoughts about the future of Russia seize them.
Meanwhile, archers and Moscow folk welcome Ivan Khovansky, their leader.
Son of Prince – Andrew – pursues with his amorous claims Emma, a girl from a German settlement. His last love, dissident Marfa, rises on her protection. Ivan Khovansky also liked Emma. In Khovansky's dispute for a girl it comes to a fight, but the head of dissenters Dosifej does not allow the tragedy to burst.
The Cabinet of Prince Vasily Golitsyn – the chancellor and Sofia's former favourite.
Prince is immersed in gloomy meditation, the fear of the future overcomes him.
Under the pretext of a guessing Marfa warns the prince about forthcoming dangers and fast disgrace. Superstitious Golitsyn is in confusion. To avoid publicity, he orders to drown Marfa, but she manages to escape.
Peter's opponents, Ivan Khovansky and Dosifej, gather for council at Golitsyn: they should agree with "division" of board in Russia. Dosifej stops the quarrel of contenders Golitsyn and Khovansky. He encourages them to restrain their arrogant pride, to think about saving Russia.
The dissenters pass by Golitsyn's house, and Marfa comes running into the cabinet. Exposing Golitsyn, the girl tells how Peters people saved her from death. Appearance of Shalkovity is no good for the gathered: his message is terrible. King Peter has learnt about the plot, condemned Khovanshchina and ordered to find instigators.
Marta gives vent to her grief in a song, remembering the painful and already unrequited love for Andrew. Dosifej consoles the girl with warm sympathetic word. It predicts to dissenters death on fire. Time for self-burning has not come yet, considers Dosifej.
Shalkovity sees himself as the elect which is on forces to relieve the country from infinite sufferings. For this purpose all means are good.
Drunk riflemen indulge in violent fun. Their wives attack drunk husbands gone on a spree. Kuzka-archer "starts a song about gossip." Terrified Podyachy reports about trouble: Peter’s people and Reiters(hired riders) have attacked Streletsky settlement and they do not spare neither old, nor small persons. The charge against Khovansky pours out in revenge to his assistants – riflemen.
Archers are stunned. They ask Khovansky to lead them in the fight against Peter’s people. But the fear of royal disgrace compels the prince to call archers to submit and go home.
Ivan Khovansky's tower.
During the meal, hay girls and Persian dancers try to entertain the prince singing and dancing.
Golitsyn's servant warns him about danger. Khovansky orders to whip him – nobody would dare to disturb the prince in his possession!
The messenger of princess Sofia – Shaklovityj – invites the prince to Privy Council. Khovanskii dresses in ceremonial dress and goes to an exit under glorification of girls. On a threshold a dagger of the murderer hits prince. It is Shaklovityj eliminates competitors.
The prediction of Marfa has come true – Golitsyn was sent into exile. The other opponents of Peter have also unenviable destiny: the execution of archers is already appointed on the Red Square and reiters are sent to a dissenting monastery. Andrew does not believe in a plot failure, but archers don’t respond on his trumpet call. Marfa tells him that his father – Ivan Khovansky – is killed. Seeing, as shots are conducted on execution, Andrew realizes that death is inevitable. In fear, he asks Marfa to save him.
On Red Square boyar Streshnev is reading to already prepared for execution riflemen the order of prince Peter about the pardon.
Night near dissenting monastery.
Dosifej grieves, understanding the doom of dissenters. He appeals to brotherhood with a call to burn in the fire in the name of the holy faith, but not to give up. Dissenters are ready to give themselves up to burning. Andrew and Marfa, who dreamed of reunion with her beloved in death, die together with their brethren.