A beautiful woman is running through the woods, constantly looking over her shoulder. She falls into a smoking crevice in the ground and is hanging on for her life, but is saved by Hercules. Suddenly the woman awakens in her bed, and has just had a dream, saying only, "He's coming."
Hercules is traveling on a ship captained by Demetrius. A storm blows up on the horizon, but before the sailors can prepare, the ship begins to be torn apart. A fire spreads, and Hercules is knocked overboard. He is awakened on a beach by Cassandra, the same woman who had the dream, and Hercules is seemingly the lone survivor. She tells him he is on Atlantis. Taking him back to her home, she reveals that she knew he was coming because of her dreams, which she claims are visions that always come true. Cassandra also reveals that her visions show Atlantis being destroyed. Hercules does not seem to believe her, but he wants to help her anyway. Being an outsider, she needs him to come with her to the council. On the way, they see gliders flying through the air, and an advanced city in the distance. Atlantis is far more advanced technologically than Hercules has ever seen.
In the city, gadgets and devices are on display everywhere and are shown to be powered by crystals that react in the sun. The people treat Cassandra badly, and refuse to speak or deal with her. She says she lives without the devices of others, and is seen as an outcast. At the same time she mentions Atlantis has not believed in the gods for centuries, but hearing that Hercules is a half-god, her beliefs about the "myths" are confirmed. At the council, King Pantheus hears Cassandra's warnings, but dismisses them as ridiculous and banishes her and Hercules from the city.
At night, Cassandra wakens Hercules with another vision, this one of fire. As she says this, citizens from the city have come to her home and thrown torches, setting it on fire. Hercules saves her, and scares the citizens off when he crashes through the flames. The leaders of the mob relate this to the king, as he seems to have sent them in the first place. Worried, he sends guards to bring Cassandra and Hercules to him. The guards subdue him with crystal-powered lances, and he is brought in powered cuffs to the king. Thrown in a cell that shoots random crystal-powered fireballs, he uses them to break the cuffs and escape.
The king uses mirrors to duplicate Hercules "trick" of walking through fire and placates the citizens. He then tries to use Cassandra as an advisor, but she does not know how Atlantis will be destroyed. He thinks she is lying, and uses a crystal torture device to get it out of her. Meanwhile, Hercules free's the slaves in the mines under the city, and among them are Demetrius and other shipwrecked crewmen. They steal a ship in the harbor, and agree to wait for Hercules until the island is destroyed.
After fighting off some guards in gliders, Hercules rescues Cassandra as the city collapses on itself. It seems that island was being mined out for crystals by King Pantheus, causing it to sink. After another fight with guards, Cassandra and Hercules leave the city by glider as the palace falls in and kills the king. Behind them, the city sinks into the sea. In the distance, Demetrius' crew convinces him to leave Hercules, but he and Cassandra soon land the glider and sail off back to Greece, with the two agreeing to be friends for a long time.