Several people are viewing a museum collection. Called the Quallus Collection by the guards, the people are being ushered out for closing. A guard thinks he sees a statue of Hermes move slightly, but dismisses it and leaves. Once the doors are shut, flames rise up around a green stone in the middle of the room. The Hermes "statue" then gets down off its pedestal, and shakes off the makeup, revealing himself as Autolycus, the King of Thieves. He is here to steal the green stone.
Hercules is in a nearby village, repairing things around the town. It is shown to be the same village he lived near with Serena, and he feels a connection to the place and wants to help out. He offers to fix a broken well, but is told it is a sort of shrine to a child who fell into it and died. Falafel has set up a stand in the market, and is attempting to sell an hourglass egg timer called the "falafelometer." Some men try to take his chickens, and Hercules defends Falafel. Meanwhile, the museum guards have figured out they had no statue of Hermes, and go to stop Autolycus, who is suspended above the green gem, called the Cronus stone. As he is about to be hit by an axe thrown at him, Autolycus yells "Stop!", and the stone freezes time. Except as a half-god, Hercules is unaffected, and wanders around the scene of the fight as everyone is suspended mid-motion.
Seeing Autolycus leave the museum, he hides amongst the stopped people. Autolycus walks through and sees Hercules, thinking he is stopped in time too. When he sneezes though, Hercules says "Bless you" and reveals himself. To get away, Autolycus selectively unstops the men that were fighting. The King of Thieves begins to ponder what he can do with the stone, and thinks that it would have been more of a challenge to steal the stone when King Quallus was alive. As he is thinking this, Hercules catches up to him, and grabs the stone. Suddenly they are taken back in time, to five years before. A man on horse rides through and destroys the stone, leaving Hercules and Autolycus stuck in the past.
They figure, though, that the stone from this time period is still there, and all that has to be done is have Autolycus steal it again. Hercules reminds him not to interfere in the timeline, but he himself saves a little boy from falling into a well. This was the same boy whose death caused the well in the future to be a shrine. Excusing this act, they decide not to interfere further and just steal the stone and go back. Outside of the village though, Hercules sees thunderclouds forming, and guesses it has to do with Zeus. He parts with Autolycus to investigate.
In the hills, the Golden Hinds are being wiped out by Zeus, fearing their god-killing blood. Serena comes upon the scene in Hind form, and is changed into human form by Ares to save her. He and Strife had been watching the destruction nearby, and decided to save her so they could use her. Hercules sees all this, and is noticed by Ares, who just laughs.
At the museum, Autolycus is about to take a secret passage when he is interrupted by his past self, coming to steal the stone. The future Autolycus knows the past one will fail, so they team up to steal it together. They are both caught anyway. Taken to King Quallus, who is convinced they are twins, they are thrown in jail to await execution.
Meanwhile, at Ares' temple, Hercules finds the god watching a confused Serena. Ares notices his half-brother looks older, and guesses he is a time-traveller. He reveals he wants to keep her around without Zeus knowing, but Hercules reminds him if Zeus finds out, he won't be spared the wrath. Near the temple path, Serena finds an injured hunter and his brother. She uses her healing powers on him, and when asked what happened, they revealed they were hunting the Golden Hinds. During her outrage, a hunter touches her and she changes into the Hind. Before anything can happen, Hercules saves her. Not sure what to tell her, he tries to convince her she doesn't need Ares. Confused, she runs away. In the woods, she is shot by an arrow. Ares comes up and helps her, and wants her to stay with him so he can teach her to defend herself. She mentions Hercules, and the god stifles his anger, telling her he will be there if she wants his help.
At the temple, Ares is holding the arrow coated with Hind's blood. He reminds Strife that they cant use it on Hercules, and muses that this may be why he came back in time. Strife wants to use the arrow though, and Ares leaves it right in front of him. In the woods, Strife shoots Hercules with the arrow. Dying, Serena comes along and heals him. She senses something during the healing, and feels she has a destiny she must discover for herself. Hercules asks her to sleep on it, and she leaves.
Both the Autolycus' escape from prison and set up camp for the night. They begin to argue and fight, and Hercules finds them both, being momentarily confused by the site of the identical Kings of Thieves. The past one acts arrogant and rude, and is then knocked out and tied up by the future one, who goes to steal the stone by himself. Getting the jump on the guards, Autolycus is able to steal the stone as King Quallus is convinced the other one is near and that this is a distraction.
At the temple, Ares is angry at Strife for trying to kill Hercules, and failing. He decides that the only thing to be done is kill Serena. Finding she and Hercules together, Ares stabs her and starts fighting the hero, wielding the Hing-blood covered knife. Hercules bests the god in the fight, and holding the knife to his throat, gets him to make the Hind mortal, saving her life. Ares and Strife disappar, and Hercules and Serena go to the village.
At the village, a boy run into Serena. Not only does she not change into the Hind, but she is unable to heal the boy, who hurt himself slightly when he ran into her. Autolycus arrives with the stone, and Hercules says goodbye to Serena, happily knowing she is alive, but realizes she won't remember him in the future. Back in their own time, Hercules smashes the stone, much to Autolycus' disappointment. A little girl runs into him, and Serena appears, coming after her daughter. She has made the village her home, and has a husband too, but doesn't remember Hercules. Autolycus notes that Hercules gave her life back to her, but in the process, wiped out their whole relationship. Hercules says its the "best thing that never happened" to him.