The novel has two settings. The first is Moscow during the 1930s, where Satan appears at Patriarch's Ponds as Professor Woland. He is accompanied by Koroviev, a grotesquely dressed valet; Behemoth, a black cat; Azazello, a hitman; and Hella, a female vampire. They target the literary elite and Massolit, their trade union,[note 1] whose headquarters is Griboyedov House. Massolit consists of corrupt social climbers: bureaucrats, profiteers, and cynics. The second setting is the Jerusalem of Pontius Pilate: Pilate's trial of Yeshua Ha-Notsri (Jesus of Nazareth), his recognition of an affinity with (and spiritual need for) Yeshua, and his reluctant acquiescence to Yeshua's execution. The Jerusalem plot of the novel is later revealed to be the novel written by the Master.
Part one opens with a confrontation between Berlioz (the head of Massolit) and Woland, who prophesies that Berlioz will die later that evening. This interaction between Woland and Berlioz is mirrored by the trial of Yeshua by Pontius Pilate. Woland entrances Berlioz in the story that leads up to Yeshua's execution. In the story, Yeshua is presented as having inhuman characteristics. Woland tells this story to convince his audience of God's existence, but the two Soviet authors refuse to believe him. The Professor also predicts the way Berlioz will die, saying that his head will be cut off by a Russian woman, and that it must happen, because 'Annushka has already brought the sunflower oil.' Although Berlioz dismisses his death prophecy as insane raving, he slips on the spilled oil and has his head decapitated by a tram car driven by a Russian woman, dying in the same way that the professor predicted. In fact, shortly before Berlioz's accident, Woland informs the two writers that "there exists a seventh proof" of the devil's existence, so in this way the predetermined nature of Berlioz's death is framed as proof of both God's and the devil's existence. The fulfillment of his death prophecy is witnessed by Ivan Nikolaevich Ponyrev, a young, enthusiastic, modern poet who uses the pen name Bezdomny ("homeless"). His nom de plume alludes to Maxim Gorky (Maxim the Bitter), Demyan Bedny (Demyan the Poor), and Michail Golodny (Michail the Hungry). His futile attempts to capture the "gang" (Woland and his entourage) and his warnings about their evil nature land Ivan in a lunatic psychiatric clinic, where he is treated by Stravinsky, a local doctor. The care he receives in the clinic is very good, especially by the standards of the time. It thus serves as an important place in the novel for many characters whom Woland confronts, and derives special importance from its bringing together of Ivan and the Master, an embittered author whose name connects to the title of the text. Master explains to Ivan that the rejection of his novel about Pontius Pilate and Christ led the Master to burn his manuscript in despair and turn his back on Margarita, his devoted lover.
In Moscow, Woland and his retinue put on a show at the Variety theater. During the show master of ceremonies Bengalsky's head is ripped off then reattached at the urging of the audience. The audience is amazed when Koroviev makes money rain down and when Woland's retinue gives out luxury fashion items to the women of the audience. Later the money and clothes disappear, causing chaos and embarrassment. Here, Bulgakov portrays women's and men's sins very differently. The women of Moscow are condemned for accepting free clothing, while the men are condemned for adultery, excessive greed, etc., and the two are portrayed as equivalent transgressions. During this performance, Woland notes the lack of moral progress made in Soviet society, remarking that despite their technological advancements such as "buses, telephones, and other [apparatuses]," Muscovites remain "people like any other people... they love money, but that has always been so." The key difference between the Muscovites Woland observes now and the Muscovites of the past is believed, by Woland, to be due to the housing crisis in Moscow. Woland cites the "housing problem" as what has corrupted these Muscovites to an even further level than what Woland has noted in the past. This scene is a key moment in Bulgakov's societal criticism.
The story returns to Jerusalem, where Ivan dreams of the execution of Yeshua as witnessed by Matthew Levi. The dream opens with Yeshua and two other prisoners, who are making their way to Bald Mountain, where they will be executed by being hung on wooden posts. In an attempt to save Yeshua from a torturous death, Levi steals a knife to kill him quickly, but he is too late to reach Yeshua. Yeshua hangs on the cross and suffers in the excruciating heat for hours until an executioner offers him some water and kills him, by stabbing him in the heart with a spear. As he dies, a great storm appears, filling the sky with thunder and lightning and raining heavily down on the people below. Levi cuts down the three bodies of the dead prisoners, before putting the body of Yeshua on his shoulder, and carrying it away.
Back in Moscow, after Woland's performance, the city is thrown into confusion. At the Variety Theatre, the highest-ranking employee left is Vassily Stepanovich, the bookkeeper. His attempt to make sense of the show's aftermath reveals a trail of chaos left by Woland and his retinue. Rubles are transforming into insects, bureaucrats have been replaced by animate suits, and entire offices have been cursed to break into song against their will. As a result of this chaos, truckloads of Muscovites are shipped off to Stravinsky's clinic. Similarly, Berlioz's uncle's attempt to claim his late nephew's apartment is thwarted by Behemoth and Azezello, who send him violently off. Immediately thereafter, Andrei Sokov, barman at the Variety Theatre, visits the apartment. Woland welcomes him in, offering fine food and drink, though Sokov declines these niceties. After some conversation, Woland reveals to Sokov that he will soon die of liver cancer and suggests that he spend his savings to enjoy a short life of hedonism.
Part two introduces Margarita, the Master's mistress, who refuses to despair of her lover and his work. Azazello gives her a magical skin ointment, which turns her invisible, and invites her to the Devil's midnight Good Friday ball, where Woland gives her the chance to become a witch.
Margarita enters the realm of night and learns to fly and control her unleashed passions. Natasha, her maid, accompanies her whilst riding Nikolai Ivanovich who has taken the form of a pig, as they fly over the Soviet Union's deep forests and rivers. Margarita bathes and returns to Moscow with Azazello as the hostess of Satan's spring ball. At Koroviev's side, she welcomes dark historical figures as they arrive from Hell.
Margarita survives the ordeal, and Satan offers to grant her deepest wish. She chooses to ask to free a woman she met at the ball from eternal punishment. The woman, who had been raped, murdered her child; her punishment was to wake each morning next to the handkerchief she used to smother it. Satan tells Margarita that she liberated the woman, and still has a wish to claim from him. She asks for the Master to be delivered to her and he appears, dazed and thinking he is still in the lunatic asylum. They are returned to the basement apartment which had been their love nest.
Matthew Levi delivers the verdict to Woland: the reunited couple will be sent to the afterlife. Azazello brings them a gift from Woland: a bottle of Pontius Pilate's (poisoned) wine. The Master and Margarita die; Azazello brings their souls to Satan and his retinue (awaiting them on horseback on a Moscow rooftop), and they fly away into the unknown, as cupolas and windows burn in the setting sun, leaving Earth behind and traveling into dark cosmic space. The Master and Margarita will spend eternity together in a shady, pleasant region resembling Dante Alighieri's Limbo, in a house under flowering cherry trees.
Woland and his retinue, including the Master and Margarita, become pure spirits. Moscow's authorities attribute its strange events to hysteria and mass hypnosis. In the final chapter, Woland tells the Master to finish his novel about Pontius Pilate – condemned by cowardice to limbo for eternity. The Master shouts "You are free! He is waiting for you!"; Pontius Pilate is freed, walking and talking with the Yeshua whose spirit and philosophy he had secretly admired. Moscow is now peaceful, although some experience great disquiet every May full moon. Ivan Ponyrev becomes a professor of philosophy, but he does not write poetry anymore.
