The scene is set at the Temple of Isis and Osiris and in the realm of the Queen of the Night, in legendary times.

A young prince, Tamino, is pursued by a giant serpent while hunting near the Temple of Isis. As Tamino falls unconscious, three Ladies, attendants of the Queen of the Night, appear and slay the beast. The three Ladies quarrel over who should stay to guard the Prince, until finally all three leave to tell their mistress about the handsome stranger. Papageno, a bird-catcher, arrives with his cage of birds just as Tamino awakens to find the dead serpent. Papageno boasts that it was he alone who killed the beast; whereupon the three Ladies reappear and punish the liar by padlocking his mouth. They also present Tamino with a locket containing a portrait of Princess Pamina, the daughter of the Queen of the Night. Tamino, who falls in love at first sight with Pamina, is told that she has been abducted by the evil sorcerer Sarastro. Just then, amid a great rumbling, the Queen appears out of the darkness and calls upon Tamino to rescue her daughter from captivity, promising him Pamina’s hand in marriage as a reward. The three Ladies give Tamino a magic flute to protect him and remove Papageno’s padlock, giving him a chime of magic bells as protection and orders to accompany Tamino upon his adventurous mission. Tamino and Papageno are further promised the guidance of three Spirits along the way.

Princess Pamina, who has just attempted to escape Sarastro’s palace, is caught by Monostatos, the slave-master. When Papageno stumbles upon them, his outlandish appearance frightens Monostatos away. Papageno reassures Pamina that Tamino is on his way to rescue her but first they must escape from the palace.

Meanwhile, the three Spirits have led Tamino to a sacred grove, where he attempts to enter the Temples of Reason and Nature but is rejected. Upon knocking at the Temple of Wisdom, an old priest, the Speaker, informs him that he has been misled, that Sarastro has good reason to abduct Pamina and that the Queen of the Night is the evil one. When voices announce that Pamina is still alive, Tamino joyfully plays on his flute. He immediately hears a reply from Papageno in the distance and runs off to find him. Just then, Papageno and Pamina enter from the opposite direction, pursued by Monostatos, who is eventually rendered harmless by Papageno’s magic bells. Sarastro enters with his Priests to the sounds of a chorus of praises. Pamina confesses that she tried to escape because of Monastatos’ lust for her. Sarastro informs Pamina that she will soon be freed but warns her against her evil mother. When Tamino is led in as a captive by Monostatos, Sarastro orders that Monostatos be beaten rather than praised for his deeds. Meeting for the first time, Tamino and Pamina swear their love for each other but are separated immediately as Tamino and Papageno are led away to be initiated into the mysteries of the Temple and the brotherhood of Sarastro.

The Priests file in as Sarastro announces Tamino’s candidacy for initiation, and they all praise Isis and Osiris. The Priests ask Tamino and Papageno if they are willing to undergo the trials. Papageno reluctantly agrees, only after being promised a beautiful young lady as reward if he succeeds. The first trial they encounter is to remain silent. After the Priests leave, the Queen’s three Ladies appear and try to turn Tamino and Papageno against Sarastro by warning that the Queen, who is nearby, has commanded them to rescue Pamina for her. The three Ladies, hearing approaching voices, flee in fear.

Alone and sleeping in a garden, Pamina is about to be molested again by Monostatos when the Queen appears to give Pamina a knife with which to kill Sarastro. Monostatos tries to seduce Pamina by blackmailing her with the information he overheard the Queen tell her. Sarastro reappears, sends Monostatos away and tells Pamina what real love is all about.

The Priests once again enter with Tamino and Papageno, who are warned to continue to remain silent. Soon, an old woman appears to Papageno with a beaker of water. Papageno speaks to her and finds out that she claims to be his sweetheart. Before he finds out her name, the old woman disappears at the sound of a great clap of thunder, and the frightened Papageno once again swears to keep his vow of silence. The three Spirits appear in order to return the magic flute and bells, which Tamino and Papageno had lost. Pamina enters and finds the silent Tamino, who motions that she must leave. Pamina, unable to understand Tamino’s actions, decides that death might be the only solution to her despair whereupon, she leaves. Hearing three trumpet calls, Tamino and Papageno leave to follow the sounds.

Sarastro commends Tamino on his conduct so far but warns that two more trials remain. Pamina is brought forth in order to say farewell to Tamino. Papageno, alone for the first time, sings of his longing for a woman to share his life. The old woman enters and is transformed into Papagena, but Papageno is told by the Speaker that he is not yet worthy of Papagena.

The three Spirits appear and prevent the distressed Pamina from committing suicide. She is then brought to Tamino, with whom she successfully undergoes the trials of fire and water with the aid of Tamino’s magic flute.

Papageno, alone and sad, is about to hang himself when the three Spirits stop him and present Papagena to him. Papageno and Papagena declare their love and plan their future family together.

Monostatos, the Queen and her three Ladies appear in darkness and plot to overthrow Sarastro. Suddenly, the scene is filled with bright sunlight, and Sarastro is seen standing with Tamino and Pamina dressed in priestly robes. The Queen and her cohorts vanish as they realize that light has triumphed over darkness and the power of evil. The Priests sing a chorus of praises to Isis and Osiris and the victorious couple.