Grieving over the loss of Iolaus, Hercules vows to persuade the Sumerian gods to bring him back from their underworld. Reluctantly accompanied by Nebula, he sets off on his quest, but many things stand in their way.
Hercules, having lost his confidence, is washed up on the island of Eire, where Druids claim he is their "Chosen One," brought to them to deal with an evil demigod who is out to destroy them with the help of the horned god Cernunnos.
Salmoneus and Autolycus wind up in possession of a sultan's lamp and release a genie who grants them three wishes. But they soon learn to be careful what they wish for. Meanwhile, the sultan wants his lamp back.
Hercules, still in Eire, is teaching Morrigan to face her new role as guardian of Justice, when Caesar prepares to attack the isle. Herc leads the locals and Morrigan in defending the island.
Hercules, having had a vision that he must save a man's life, heads to Norway, where he learns that the man is in fact the Norse God Balder. Soon he becomes entangled in an end-of-the-world prophecy.
Hercules is enjoying life in Eire, where he is getting close to Morrigan. But visions of Nebula in danger lead him and Morrigan back to Sumeria, where they find Nebula on the brink of insanity after visions of the dead Iolaus.
Studio head B.S. Hollingsfoffer orders the producers and writers to come up with better stories for the series, so they head off to a corporate retreat camp, but once there, someone keeps trying to kill them.
Hercules returns to Greece with Morrigan and Nebula in pursuit of Dahak who, in Iolaus' body, has convinced the locals he is their savior and Hercules is out to destroy them. Herc must find a way to separate Dahak from Iolaus.
Hercules, with Amazon Ephiny, recruits a rag-tag band, including a murderer, in a mission to use explosive crystals to blow a hole in the side of a volcano and stop lava from destroying a town in its path.
Hercules travels back to the Alternate Universe, where Iolaus' parallel double joins him in trying to free the gods of Olympus, whom Ares has entrapped.
Hercules, missing the original Iolaus, tells Iolaus II of an adventure where he and Iolaus had to retrieve a stolen ruby from Autolycus, who had a curse looming over him until he returned it.
Morrigan returns and joins Hercules on his mission to save the Oracle of Cyprus from a wronged soul who has returned from the grave to destroy her. As they travel, Hercules learns why Morrigan suddenly left him.
Hercules and Jason return to their old academy with Iolaus II, where they find the place in chaos as a group of renegade cadets are taking over the running of the school. Meanwhile, Jason finds he has a daughter he never knew existed.
With Hercules away on a mission, Iolaus II admits to Aphrodite that he longs to experience love. Meanwhile, Discord turns Nautica the mermaid into a beautiful woman, and soon Nautica and Iolaus fall in love.
In 500 A.D., Merlin sends tyrannical Arthur of Camelot back to Hercules' time for the half-god to set him straight. Younger Merlin leads Herc to Britannia to team up with Morrigan and stop Arthur and his sorceress accomplice.
A scheme by Ares, Discord and Ares' new lackey Deimos has cursed a whole village into starting to fade out of existence. When Hercules breaks the stone that has caused the curse, he starts to fade away.
Iolaus II is shocked to learn that Nautica is being forced into marrying a goon. Hercules runs into his former wife Serena. With Aphrodite's help, the two learn that the goon had stolen the trident which belongs to Nautica's father Triton.
Iolaus returns from beyond the grave to warn Hercules that the end of the world is at hand. The Archangel Michael is bringing about the apocalypse by releasing the Four Horsemen onto the land.
