The King of Priam’s daughter, Ilia, contemplates the defeat of Troy, and thinks about her loved for Prince Idamanante, Idomeneo’s son. When Idamanante arrives to free the Trojan prisoner, Ilia rejects him and he tells her they have no fault in their father’s hate for each other. Elettra protests Idamante's clemency toward the prisoners. Idomeneo has been lost at sea on his return voyage and Elettra, fears that a Trojan soon will be Queen of Crete. Shipwrecked Idomeneo recalls the promise he made to Neptune to sacrifice, if he were spared, the first living creature he meets on shore. Idamante approaches him but they don’t recognize each other right away. When Idomeneo realizes he orders Idamante never to seek him out and the son, hurt, leaves.
Padre, germani, addio!, Ilia's Aria
Non ho colpa, Idamante's Aria
Tutte nel cor vi sento, Elettra's Aria
Arbace, Idomeneo’s counsellor, says that if Idamante went into exile immediately, they could find a substitute to sacrifice. Idomeneo orders his son to escort Elettra home to Greece. Ilia declares that since she has lost everything, he will be her father and make Crete her country. Idomeneo realizes his rescue has cost Ilia her happiness as well as his own. Elettra will be going to Argos with Idamante, so she can declare him her love. Before the ship can sail, however, a storm breaks out, and a sea serpent appears from the water. Recognizing it as a messenger from Neptune, the king offers himself as atonement for having defaulted in his bargain with the sea god.
Se il padre perdei, Ilia's Aria
Fuor dal mar, Idomeneo's Aria
Ilia hopes for Idamante to survive the storm and confesses him her love while they are heard by Elettra and Idomeneo, who rushes his son to leave. Meanwhile, the High Priest of Neptune tells the king of the destruction wrought in the land by Neptune's monster, exhorting Idomeneo to reveal the name of the person whose sacrifice is claimed by the god. When the king confesses that his own son is the victim, the population is horrified. Outside the temple, the king and High Priest join with Neptune's priests in prayer to praise the god when Arbace announces that Idamante has succeeded in killing the serpent. Idamante enters in sacrificial clothes and is ready to die in sacrifice. Idomeneo is about to sacrifice his son when Ilia intervenes, offering her own life instead. The oracular Voice of Neptune speaks: Idomeneo must yield the throne to Ilia and Idamante. Idomeneo, relieved, presents Idamante and his bride as the new rulers.