Long ago, three Olympians—Zeus, Poseidon, and Hades—battled the Titans. Hades provided their means of defeating the Titans with his creation, the Kraken. After the Titans' defeat, Zeus created land-animals (including humans) and ruled them while Poseidon ruled the sea and its creatures. But Zeus deceived Hades and forced him to rule the Underworld. Zeus and his fellow gods on Mount Olympus rely on the prayers of humans to sustain their power.
Millennia later, a fisherman named Spyros finds a coffin adrift in the sea. In it are infant Perseus and his dead mother, Danaë. Spyros raises Perseus as his own son. Years later, the adult Perseus and his family are fishing when they witness a group of soldiers from Argos destroying a massive statue of Zeus as a declaration of war against the Gods. Hades takes the form of harpies to massacre the soldiers. In the battle, Perseus' family's fishing boat is destroyed, killing all except Perseus. The surviving soldiers take Perseus back to Argos. During a feast for the returning soldiers, King Kepheus and Queen Cassiopeia of Argos compare themselves and their daughter Andromeda to the goddess Aphrodite, much to their daughter's dismay. Having convinced Zeus to punish Argos, Hades appears in the courtroom, kills the remaining soldiers and ages Cassiopeia to the brink of death. Recognizing that Perseus is the Demigod son of Zeus, Hades threatens that if Princess Andromeda is not sacrificed to the Kraken, Argos will be destroyed in ten days. Hermes, the Messenger God, informs Zeus that Perseus is in Argos and suggests offering him sanctuary. Zeus refuses.
The King imprisons Perseus because he will not fight with Argos against the gods. Io, a woman who does not age as punishment for refusing to be seduced by the God Ares, reveals to Perseus his true lineage: in order to punish King Acrisius for his own war on the Gods, Zeus disguised himself as Acrisius and seduced Danaë, impregnating her. When Acrisius set Danaë and the baby Perseus adrift in their coffin, an enraged Zeus struck Acrisius with lightning, leaving him hideously disfigured. After learning that killing the Kraken would allow him to have his revenge against Hades, whom he blames for Spyros's death, Perseus agrees to lead Argos' finest soldiers on a quest to find the Stygian Witches. They are joined by a pair of hunters named Ozal and Kucuk; Io follows as well. Hades finds Acrisius, now called Calibos, and reveals his plan to use the Kraken to destroy Argos, thereby weakening Zeus and gaining his revenge for his betrayal after the Titan battle. Hades imbues Calibos with superhuman powers in order to kill Perseus.
While in the woods, Perseus discovers a sword forged in Olympus, as well as Zeus' sacred herd of flying horses, the Pegasus. However, Perseus refuses both the sword—which only he can use—and Pegasus that the Gods were offering as assistance, as he does not wish to become a god. Calibos attacks the group and tries to murder Perseus, but is forced to flee after Draco cuts off his hand. However, Calibos' blood forms giant scorpions from the sand that attack Perseus and kill many of his group. The survivors are saved by the Djinn, a band of formerly human shamans who have turned themselves into the Demons of Arabian mythology by replacing their earthly flesh with ash and stone. Though the Argonauts do not trust the Djinn at first, Sheikh Suleiman heals Perseus' wounds, and the Djinn joins Perseus' group as they too wish to see the Gods overthrown.
The heroes learn from the Stygian Witches that the head of the Gorgon Medusa could kill the Kraken by turning it to stone. When they tell Perseus his group will die in the process, all of the Djinn except for Suleiman leave them. Perseus is visited by Zeus who offers him asylum on Mount Olympus, but he refuses. Zeus gives him instead a golden drachma, which Perseus later learns is a means to bribe Charon for passage into the Underworld. In the battle with Medusa, only Perseus survives to behead her. Emerging from the Underworld, Perseus sees Calibos stab Io. Perseus kills him using the sword from Olympus, which restores Acrisius to human form. Perseus watches as Io transforms into gold dust and is swept to Olympus. He then rides Pegasus back to Argos with Medusa's head.
In Argos the Cult of Hades plots to sacrifice Andromeda to the Kraken. As the Kraken is released, Hades reveals to Zeus that the destruction of Argos will give him enough power to overthrow the other Olympians, but Zeus reveals Perseus is still alive in Argos. Although Hades sends his harpies to kill Perseus, Perseus uses the head of Medusa to turn the Kraken into stone and rescues Andromeda. He then uses the sword of Olympus, amplified by with Zeus' lightning, to banish Hades back to the Underworld. Andromeda asks Perseus to become king of Argos, but he declines. Zeus again offers Perseus sanctuary, but Perseus rejects this as well. Warning that Hades will someday return, Zeus resurrects Io and disappears.
