The opening scene shows the troops of Agamemnon of Mycenae ready to fight against the troops of Triopas of Thessaly. Afterwards, Prince Hector of Troy and his younger brother Paris negotiate a peace treaty with Menelaus, king of Sparta, and celebrate the end of a long and bloody war. Paris, however, is having a secret love affair with Menelaus' wife, Queen Helen, and smuggles her aboard their homebound vessel, much to Hector's fury, as this could lead to war between Troy and Greece. Upon learning of this, Menelaus meets with his elder brother, King Agamemnon of Greece, and asks his help in taking Troy. Agamemnon, who has wanted to conquer Troy for a long time, agrees, since it will give him control of the Aegean Sea. On King Nestor's advice, Agamemnon has Odysseus, King of Ithaca, persuade Achilles to join them. Achilles, who strongly dislikes Agamemnon and his ways, initially refuses, but eventually decides to go after his mother, Thetis, tells him that though he will die, he will be forever remembered.
Perseus (Sam Worthington), a son of Zeus (Liam Neeson), lives as a fisherman after the death of his wife, Io (portrayed by Gemma Arterton in the previous film), with his young son, Helius (John Bell). Zeus visits Perseus and asks for his help, saying that humans are not praying to the gods and as a result the gods are losing their power and becoming mortal. Perseus realizes the walls of Tartarus are crumbling and Zeus informs him that the imprisoned Titan Kronos will soon be free. Perseus, valuing his family's safety, refuses to get involved.
After imprisoning the Titans beneath the ocean, the Greek gods gather to Mount Olympus for Zeus, and his wife Hera have a son named Hercules. While the other gods are joyful, Zeus' jealous brother Hades plots to overthrow Zeus and rule Mount Olympus. Turning to the Fates for help, Hades learns that in eighteen years, a planetary alignment will allow Hades to locate and free the Titans to conquer Olympus, but only if Hercules does not interfere. Hades sends his minions Pain and Panic to dispose of Hercules. The two succeed at kidnapping and feeding him a formula that turns him mortal, but fail to remove his superhuman strength before Hercules is found and adopted by the farmers Amphitryon and Alcmene.
Hercules (Dwayne Johnson) is the leader of a band of mercenaries comprising the spear-wielding prophet Amphiaraus (Ian McShane) of Argos, the knife-throwing thief Autolycus (Rufus Sewell) of Sparta, the feral warrior Tydeus (Aksel Hennie) of Thebes, the Amazon archer Atalanta (Ingrid Bolsø Berdal) of Scythia and his nephew storyteller Iolaus (Reece Ritchie) of Athens. Hercules is said to be the demigod son of Zeus, who completed the legendary Twelve Labors, only to be betrayed by Hera who drove him insane and caused him to murder his wife Megara (Irina Shayk) and their children during a visit to King Eurystheus (Joseph Fiennes). Throughout the film, it is not clearly established that Hercules is truly the son of Zeus, and many are skeptical of the claim as well as of the stories of Hercules' famous Twelve Labors. Despite this, Hercules is frequently seen displaying unusual strength and nigh-unmatched skill in combat. Hercules is frequently haunted by the memory of the deaths of his wife and daughters by his hand, as well as visions of Cerberus.
In ancient times after defeating their predecessors, the Titans, the gods divided the Universe among themselves. Zeus took the skies, Poseidon took the seas, and Hades was left with the Underworld upon being tricked by Zeus. The gods created the mortals, whose faith and prayers assured the gods' immortality. As time passed, however, mortals began to question them and soon resist their creators, angering the Olympians.
Before the dawn of man or beast, immortals waged war against each other in Heaven. The victors declared themselves gods while the vanquished were renamed the Titans and imprisoned beneath Mount Tartarus. The Epirus Bow, a weapon of immense power, was lost on Earth during the war. In 1228 B.C., the mortal king Hyperion (Mickey Rourke) of Heraklion searches for the bow, intending to use it to release the Titans to get revenge on the gods for failing to save his family. Hyperion captures the virgin oracle Phaedra (Freida Pinto), believing that she can use her visions to find the Epirus Bow's resting place.
In 1200 BC ancient Greece, King Amphitryon of Tiryns invades Argos. Amphitryon eventually fights rival King Galenus in personal combat, killing Galenus and seizing his kingdom. Queen Alcmene is disgusted by her husband's thirst for power and warmongering. She prays to Hera for guidance and Hera, wife of Zeus, tells her that she will allow Zeus to impregnate Alcemene with the savior of her people, a demi-god son to be named Hercules. The only other witness to this is Chiron, the queen's loyal adviser. Amphitryon names his new "son" Alcides, though Alcmene secretly acknowledges his true name as Hercules.
King Acrisius of Argos (Donald Houston) imprisons his daughter Danaë (Vida Taylor), jealous of her beauty. When the god Zeus (Laurence Olivier) impregnates her, Acrisius sends his daughter and his newborn grandson Perseus to sea in a wooden coffin. In retribution, Zeus kills Acrisius and orders Poseidon (Jack Gwillim) to release the last of the Titans, a gigantic sea monster called the Kraken, to destroy Argos. Meanwhile, Danaë and Perseus safely float to the island of Seriphos, where Perseus grows to adulthood.
The film retells the story of the Trojan War, albeit with some major changes from the Iliad's storyline: Paris of Troy (Jacques Sernas) sails to Sparta to secure a peace treaty between the two powerful city-states. His ship is forced to return to Troy in a storm after he has been swept overboard on the shore of Sparta. Paris is found by Helen, Queen of Sparta (Rossana Podestà), with whom he falls in love. He goes to the palace where he finds Helen's husband, King Menelaus (Niall MacGinnis), Agamemnon (Robert Douglas), Odysseus (Torin Thatcher), Achilles (Stanley Baker) and many other Greek kings debating whether to go to war with Troy. Menelaus, who is denied by Helen, sees that his wife and Paris are in love and, pretending friendship, plots Paris' death.
While travelling, Hercules is asked to intervene in a quarrel between two brothers, Eteocles and Polynices, over who should rule Thebes. Before he can complete this task, Hercules drinks from a magic spring and is hypnotized by a harem girl who dances the "Dance of Shiva", loses his memory and becomes the captive of Queen Omphale of Lydia. The Queen keeps men until she tires of them, then has them made into statues. While young Ulysses tries to help him regain his memory, Hercules' wife, Iole, finds herself in danger from Eteocles, current ruler of Thebes, who plans on throwing her to the wild beasts in his entertainment arena. Hercules slays three tigers in succession and rescues his wife, then assists the Theban army in repelling mercenary attackers hired by Polynices. The two brothers ultimately fight one another for the throne and end up killing each other; the good high priest Creon is elected by acclaim.
Pelias (Douglas Wilmer), misinterpreting the prophecy given to him by the god Zeus (Niall MacGinnis), usurps the throne of Thessaly by killing King Aristo and most of his family. The infant Jason is spirited out by one of Aristo's soldiers. Pelias encounters one of the king's daughters, Briseis (Davinia Taylor), seeking sanctuary in the temple of the goddess Hera (Honor Blackman) and slays her. Because the murder has profaned her temple, the angry Hera becomes Jason's protector. She, disguised as the high Priestess, warns Pelias to beware of a man wearing one sandal.
Jupiter apparaît dans les cieux sur son char. Il est rejoint par Hermès, qui court sans cesse, Il fait ensuite apparaitre les huit Muses, qui chantent et dansent. Il s'énerve, car son tonnerre, qu'il brandit volontiers, ne marche plus. Celui-ci devient incontrôlable et finit par exploser.
La Terre et Perséphone vivent dans un lieu d'éternel beauté où règne toujours le printemps, entourées par des animaux et des elfes. Mais Hadès, dieu des enfers, kidnappe Perséphone et l'emmène parmi ses démons. La Terre sans Perséphone sombre dans un hiver glacial. Pour résoudre le problème, la Terre et Hadès se partagent Perséphone la moitié de l'année, créant le cycle des saisons.