Orestes and his tutor arrive in Argos, Greece, a miserable town full of unfriendly citizens and flies the size of bumblebees. The reader is expected to be familiar with the Greek legend back-story, though Sartre does help the reader by re-hashing the myth via conversation. Let's review it now.
Fifteen years ago, King Agamemnon was the ruler of Argos. He left for the Trojan War, and when he was gone his wife, Clytemnestra, took another lover, a man named Aegisthus. When Agamemnon returned from the war, Clytemnestra and Aegisthus murdered him together and took the throne. Agamemnon's daughter, Electra, remained with the new couple in the palace, while his son Orestes was disposed of, allegedly, for good. As you can see, this disposal wasn't effective, as Orestes is still alive. He grew up in another part of Greece, but now that he's a grown man, he's returned to his hometown to assess the current situation.
What he finds is that every citizen of Argos has been consumed with guilt over the murder of King Agamemnon. They spend all day mourning, repenting, wailing, beating themselves up, and living in utter misery. King Aegisthus and Queen Clytemnestra, consumed with shame, have imposed this repentance upon their people.
On the day when Orestes returns to Argos, they're holding their annual Ceremony of the Dead. Once a year, the people of Argos roll back a stone blocking what they believe is the gateway to hell. According to local legend, the dead come forth and haunt the living for 24 hours, before returning to the underworld.
Orestes gets most of this information from Zeus, the King of the gods, who pretends to be a mortal man. Orestes also fails to reveal his true identity, and pretends to be a traveler named Philebus. As the Zeus and Orestes converse, we get the sense that each knows who the other really is.
Zeus is anxious to get Orestes out of Argos; he fears that the young man is seeking vengeance against the man who murdered his father. Since the gods are pleased to have a kingdom full of miserable penitents, Zeus would rather keep Aegisthus in power. But Orestes explains that he's not interested in vengeance. He has no ties to what happened in Argos. In fact, he has no meaningful memories or childhood or connections to anything, which bothers him. He feels as though he has no responsibilities or commitments.
After his conversation with Zeus, Orestes meets Electra – his sister. Again, he holds off on revealing his true identity. As the story goes, Electra remained behind in the palace with Aegisthus and Clytemnestra after her father was slain. It seems they have made her into somewhat of a servant; she resents them deeply. She also has a major beef with Zeus, whom she believes is an empty image with no substance. She predicts that a man will come one day and will reveal this to the world.
Interrupting Electra's rant is Clytemnestra, otherwise known as Electra and Orestes's mother, the Queen of Argos, and the wife of Aegisthus. She and her daughter have a pretty bad relationship, probably because Clytemnestra killed Electra's father and now treats her daughter like a slave. The Queen orders Electra to attend the Ceremony of the Dead later that day. Before the women leave, Electra advises that Philebus (a.k.a. Orestes) stick around, as the day promises some entertainment.
This sounds good to Orestes, who changes his mind and decides that he will stay in Argos. Zeus, probably in an attempt to keep an eye on the young man, offers to act as his guide. Together, the two (along with Orestes's tutor) attend the ceremony.
As Electra promised, the ceremony is indeed an interesting one, mostly because she shows up halfway through in an inappropriate white party dress (instead of the mandated black conservative funeral attire). She proceeds to dance on the temple steps while explaining to the townspeople that, actually, there are no invisible ghosts running around and tormenting them. While hesitant at first to listen to this "blasphemy," the townspeople become curious. What if Electra is right? However, Zeus is in attendance, and he soon silences Electra by crashing a huge boulder into the temple steps. The townspeople scream, "Burn the witch!", and Electra is quickly exiled.
After the crowd disperses, Orestes offers to take Electra away from this awful place. When she refuses, he reveals his true identity. Electra is a bit disappointed; she thought Orestes was going to be a raging, angry man who would ride into Argos with determination and gut the King and Queen. No, says Orestes, this wasn't his plan. He's a lover, not a fighter.
But then Orestes spends some time thinking. If he's so bothered by having no obligations, commitments, or loyalties, shouldn't he choose to commit himself to something? And what better action to commit himself to than killing the lecherous couple that murdered his father? OK, he says, turning to Electra, let's do it.
So the siblings sneak into the palace. While they're hiding out, waiting to make their move, they witness Zeus conversing with Aegisthus. The King of the gods reveals to the King Aegisthus that Orestes and Electra are planning to kill him, and he orders that they be thrown into jail. But Aegisthus refuses. He's tired of living his life miserable and repentant, and he'd rather just die. Besides, why is Zeus all concerned for the life of Aegisthus if he did nothing to save the life of Agamemnon fifteen years earlier? What's the difference?
Zeus explains that he's not trying to protect Aegisthus, nor is he concerned with justice. The gods like having people miserable and penitent. They encourage crimes if the criminals will spend their lives in remorse – as Aegisthus has done. Orestes, on the other hand, is a special case. He has figured out that man is free. Because he realizes this, he will feel no remorse for his actions. Zeus also reveals that he is powerless to do anything against Orestes: once a man realizes that he is truly free, the gods have no control over him.
Zeus leaves. Electra and her brother pop out of hiding and Orestes promptly slays Aegisthus. Before he dies, Aegisthus tells Orestes to beware of the flies. Electra starts freaking out; shouldn't they feel guilty over their crime? No, says Orestes, they should not. He promptly goes to slay the Queen, though Electra refuses to help. After both husband and wife are dead, Electra and Orestes flee to the temple of Apollo, which serves as a sanctuary for criminals in Argos.
At the temple, the siblings try to sleep, but are surrounded by the furies, a larger, meaner, and more human version of the flies, which plagued the characters in the first two acts of the play. (Sartre describes these furies as the goddesses of remorse.) Orestes seems immune to their taunting, but Electra is not. She engages them, though Orestes warns that this only gives them power over her. Electra's guilt is even manifested physically – the furies tear and ravage her face while she sleeps.
Zeus shows up and calls the furies off for a minute. He offers Orestes and Electra a deal – spend their lives in remorse, and he'll put them on the throne of Argos and keep the furies away from them. Orestes refuses, and the two of then launch into a lengthy debate on the nature of freedom, the gods, and man's place in the world.
This conversation represents the philosophical heart of The Flies. In it, Zeus argues that he is the god of the universe, and that Orestes is an insignificant bug. Orestes counters that Zeus may be the god of all creatures, the elements, and nature, but he is not the god of man. Zeus chose to make man free, and that was his big mistake. Zeus thinks it's odd for a man clinging to a criminal sanctuary to be speaking of freedom, but Orestes doesn't think so. Freedom is in the mind – it is the knowledge of one's freedom to choose and act – and not a physical state. Even a slave on the cross is free if he recognizes his own freedom.
Orestes now wants to open the eyes of the citizens of Argos the same way his own eyes have been opened. Zeus points out that the citizens of Argos are ready to stone Orestes to death. Freedom is a burden, he says, and bestowing it on the general populace would only lead them to despair. Yes, it would, says Orestes, but "human life begins on the far side of despair."
At this point, Zeus admits that Orestes has him beaten. He heard that a man would one day announce the god's decline, and it seems that Orestes is that man. Before Zeus goes, however, he wins the territorial battle over Electra; she commits herself to a life of remorse and runs off stage.
Orestes now flings open the doors of the temple and addresses the angry mob of townspeople waiting for him outside. He reveals his identity – Orestes, son of Agamemnon – and owns up to the murders from the early evening. He explains that he has taken on a burden and so earned his right as the King of Argos. Yet he doesn't want to stay and rule; he wishes to be "a king without a kingdom." Still, he says, he has freed them all with his actions. He takes their sins upon his own back, so they are free from their burden of remorse. Now he will walk in the sun. Orestes exits, and the furies run shrieking after him.