In attempting to destroy Hercules by killing everyone he cares about, Lucius sets Alcmene's village on fire and then goes after Jason, and it's up to Hercules to stop his half-brother.

Ares must enter a talent show at Kora's Inn when he learns that one of the prizes would complete his set of the Chronos stones that enabled Zeus to defeat the Titans. The catch is a mortal must willingly give it to him, so with Strife and Discord in tow, he enters intent on winning and more than willing to cheat to get it, leaving Hercules and his friends to stop him.

When Herc and the gang learn that Iolaus will be sent back to prison unless he passes an upcoming test, they attempt to help him by pulling an all-night cramming session in order to help him pass.

Hercules meets Lucius, another mortal son of Zeus, who tells him that he is on the trail of Pollux on the request from Zeus himself to deliver Pollux to death for the crime of the death of Castor, their brother. Hercules agrees to join him, unaware that Castor was actually killed by Lucius, who has some ambitious plans that don't include his brothers.

When the Amazons attack the Academy with missile-like weapons forged by Hephaestus, it's up to Hercules to ensure that no one gets hurt and to figure out the real reason for the attack. The real threat is actually Ares, who has Cyane under his control and is orchestrating all of this for one reason: to destroy Hercules.

Strife tricks Hercules into removing a vase from Hera's cave.

The trio stumbles across the Amazons once again, and this time they invite the ladies back to the Academy. Unfortunately, when they get there, the King of Athens arrives, claiming the Amazons are his property. This revelation doesn't sit well with the Amazons or Hercules, who must try to solve the situation without anyone getting hurt.

With hatred growing and the facts distorted by lies manufactured by Discord and Strife, Hercules and his friends are running out of time to prevent a war that isn't necessary and to save two people Hercules cares about.

After Ares attempts to kill Hercules yet again, he is put on trial by the gods for violating Zeus's order of protection. Ares proceeds to claim he is innocent and asks Hercules to defend him, baffling Hercules, who reluctantly decides to defend Ares.

Hercules and Jason travel to the underworld in an attempt to talk Hades out of sending Eurydice to Tartarus despite her service to Bacchus. Meanwhile, Jason is reunited with his father in the Elysian Fields.

Hercules meets Nemesis, the assassin of the gods, and talks her out of blindly killing a mortal just because Hera tells her to. The two then fall victim to Hera, who sends a replacement killer after both of them.

Jason has cold feet about his ability to lead Corinth and runs away, finding himself among a group of villagers terrorized by a warlord, where he must play the hero and stop the bad guy.

When Artemis's favorite creature, a Golden Hind, is spotted, Hercules and Kora team up to try to keep the beautiful and rare creature out of the fatal hands of the hunters who are tracking her, as well as keep her away from two other hunters, Jason and Iolaus.

After Hercules is bested in a practice sword fight by Jason, he asks Hephaestus to build him some new weaponry. Hercules's new sword and shield are made from a metal that no other metal can harm, and this power brings Hercules a lot of trouble and threatens his friendships with Iolaus and Jason.

Hercules and Iolaus set out with Jason to negotiate peace treaties between two kingdoms on the verge of war. On their way, though, they're sidetracked by Discord and Strife, who've been sent by Ares in order to distract the gang from the peace treaties. Herc and the gang come across a farmhand who bears a striking resemblance to Ares. Timor, the farmhand, reluctantly agrees to help Hercules keep Strife and Discord away from Jason by posing as Ares and keeping them on their toes.

A shrewd politician hires an assassin to kill Jason before his coronation in order to clear the path for himself to step in as king of Corinth. However, once Hercules learns of this plan, he attempts to tell everyone, but no one believes him. The problem is that it's Prank Day, and everyone thinks he's setting them up for a joke.

On the eve of Jason's coronation, a monster ravages the countryside in order to extract revenge on Jason's father for an attack made on her ten years before. Deciding on how to deal with the situation puts Jason and Hercules at odds with one another.

It's Parents Day at the Academy, and Iolaus hires two actors to pretend to be his parents so his real ones don't find out how poor his grades are and to not be disappointed in him once again. Things get complicated fast when the actors are revealed as thieves, Iolaus's real parents show up, and Hercules must keep Alcmene from discovering Iolaus's deception and revealing the truth. Meanwhile, Lilith's sister visits and announces she plans to take Lilith home.

Hercules and Iolaus meet up with a young Amazon named Mila, who is searching for the father she never knew, which Ares thinks is a great opportunity. Ares claims that he is Mila's father in order to get her under his control. His goal: he wants her to kill Hercules.

When Hercules tells his half-brother Apollo that no one really likes him—they are just afraid of him and humor him—Apollo doesn't take it well. He becomes jealous of Hercules and his friends and attacks the Academy.

Hercules, Iolaus, and Lilith are caught between friends when Discord and Strife pit Cyane's tribe and Cheiron's fellow centaurs against each other, with Cyane and Cheiron leading their armies into battle.

When a new cadet named Pythagrius claims he doesn't believe in the gods of Mount Olympus, Strife bets another god named Fatsus that he can make the cadet believe in gods. Fatsus, who can only see prophecies of bad things to come, takes that bet, and Strife's stunts cause a bigger threat as his attempts put Hercules and the academy in danger.

Hercules, Iolaus, Lilith, Theseus, and fellow cadet Marco find themselves trapped in a large area of sand known as the Dune Sea. It's known as forbidden, and for a reason too, since it is inhabited by sand sharks who hunt anyone foolish enough to enter the area. Of the five cadets who entered, one will not leave.

Hercules, Iolaus, and Jason are all sent to detention, but Hercules and Jason must cover for Iolaus when he has to leave to start his new job at Kora's.

Tired of being called a wet blanket by his friends, Hercules requests the fire in Hephaestus's Olympian forge to make him more like his father. Although at first it seems to work, by making Hercules a much more laid-back, fun guy, the side effects quickly put Hercules and his friends in danger. Iolaus and Jason must call on Hephaestus to help restore Hercules to his original self.