Clytaemnestra, in visions, recalls the sacrifice of her daughter Iphigenia and thinks of her husband, Agamemnon, in Troy and his dalliance with Cassandra. As she awakens from the last of her visions, she realizes that she has decided to kill her husband. Beacons on the horizon signal his arrival, and she goes out to greet him.
Clytaemnestra takes place primarily in Argos, shortly before Agamemnon's return from the Trojan wars. Other scenes, remembered or imagined by Clytaemnestra, occur in Aulis ten years before (the sacrifice of Iphygenia), at Troy (the prophecies of Cassandra), and in the future in Argos (the murder of Agamemnon).
The opera opens with a cry: Clytaemnestra, in a fit of grief, seeks her long-dead daughter, Iphygenia, and in a dream-like scene remembers the events that led Agamemnon to sacrifice his daughter for “reasons of state.” Clytaemnestra stops brooding and tries to persuade her lover, Aegisthus, to be less harsh towards her children. A quarrel develops and Aegisthus reveals that Agamemnon is having an affair with Cassandra, a prophetess/princess of Troy awarded to him as the spoils of war. When Aegisthus departs, Clytaemnestra imagines the scene at Troy. Agamemnon asks Cassandra to see into the future and she foretells of his death. Agamemnon fails to see the true meaning of her words, but not so Clytaemnestra: this prophecy gives her the first inkling of the dreadful deed she must carry out.
Returning to real time, Clytaemnestra's children Electra and Orestes recall happier times in contrast with the present tyranny of Aegisthus. Aegisthus enters and bullies the children, but Electra stands up to him, insultingly. Sending the others away, Aegisthus now alone with Electra, scolds her, then tries to reason with her, and finally makes an amorous advance, which she repels.
Aegisthus runs to Clytaemnestra who summons her children to attempt reconciliation. Without knowing of his advances toward Electra, Clytaemnestra tries to explain the aid that Aegisthus provides. Electra violently denounces Clytaemnestra's adultery and betrayal of Agamemnon. Clytaemnestra sends the others away and attempts to reason with Electra. Despite her words, a violent confrontation erupts which ends with Electra banished from the palace, along with Orestes.
Alone, Clytaemnestra laments the loss of her children, the death of Iphygenia, and the passing of innocence. In a final protest against the injustice of the cursed fate of women, she reaches a fevered state and collapses. Unconscious, she dreams of Agamemnon’s return and foresees his murder. She awakens knowing that this is what she must do. The beacons flare announcing Agamemnon's return.
Clytaemnestra puts aside her guilt, nostalgia, and regret, and goes triumphantly to meet a man who, as far as she is concerned, is already dead.