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With Icarus' "help," our trio of heroes sneak back into Atlantis. Of course they don't know that Icarus is leading them into a trap. They're planning to break someone out of the amphitheatre and sneak towards it through the sewer system. Pasiphae gets the news from her soldier with whom Icarus is in correspondence. Medea is horrified at the notion that Pasiphae intends to let Jason die.
The gang is able to break the prisoners out of their cells in the amphitheatre with the intention that they'll help them fight to regain Atlantis but with Icarus' betrayal, a great deal of the prisoners end up dead due to an ambush by Pasiphae's soldiers. Pythagoras immediately deduces that Icarus is responsible for this. Medea helps Jason survive the encounter but is spotted by Pasiphae's general, who relays this news to to Pasiphae.
Icarus visits his father who questions why he still hasn't been executed. Icarus doesn't want to tell him what he has done but his father knows that he is hiding something. He demands to know and Icarus finally admits what he has done. His father is disgusted by his actions and says he would rather die than have a traitor for a son, and promptly sends him out, saying he has never been so ashamed.
Pasiphae visits Medea in her room and warns her that if she doesn't stay away from Jason then she will kill her herself.
The trio and remaining ex-prisoners make it back to where Ariadne is waiting in the forest and once again, she asks Jason to marry her and this time he accepts. Hercules marries them in the middle of the forest.
Medea kills a guard and escapes from Atlantis. On her way out, she visits Jason while Ariadne is still sleeping and gives him advice on how to kill Pasiphae. She tells him to go to a particular temple which is the seat of Hecate's power and only those touched by the gods may enter. She also gives him the nectar of the passion flower that will help weaken Pasiphae's power. Medea then leaves to return to her home, now realising that Pasiphae manipulated her into becoming just like her. Medea tries to make a move on Jason once more but he pushes her off, saying he is married to Ariadne. Medea leaves and Jason relays what he has learned to the rest of the group but they still don't trust Medea. He says he is going to follow her advice and go after Pasiphae.
Hercules asks Pythagoras to open up about what is wrong, knowing that it must have something to do with Icarus, with whom Pythagoras has been romantically involved with. Pythagoras doesn't want to talk about his feelings at this time. Jason reaches the temple and finds Pasiphae there performing a ritual for the gods. He tells her he pities her since everyone she has ever loved has abandoned her. He also tells her that Medea is the one who tole him where to find her. Pasiphae tries to perform magic to kill Jason but her powers are failing her because Jason used the nectar that Medea gave him. Jason knows that he doesn't have it in him to kill her himself so he knocks her out and carries her out so others can do the deed.
When Pasiphae is brought back to the camp, she plants seeds in Ariadne's head, telling her about Jason's unfaithfulness and his fling with Medea. Jason says his goodbyes to Pasiphae and she is brought out to a clearing where Hercules executes her after she says her prayers. Jason and Ariadne plan to return to Atlantis as King and Queen. However, they must trick Cilix so they may kill him since he will never agree to what they are doing. Pythagoras suggests that they use Icarus' betrayal in order to do so. Pythagoras meets with Icarus at the cabin in the woods and confirms that Pasiphae is now dead. He also says that Jason genuinely wants to make peace and return to the city. Goran agrees to release Icarus' father and Cilix begins to make plans to take over the throne for himself.
At the meeting in the clearing, Cilix orders the men to kill the band of heroes but they end up killed before he can make his orders. Goran orders his men to stand down and once Jason throws a dagger into Cilix's back, Goran delivers the killing blow. They make an agreement that none of the men will be killed for following Pasiphae's orders so long as they swear loyalty to Jason and Ariadne as rulers of Atlantis (once they ave received the blessing of the gods). Those who do not swear loyalty will be free to leave Atlantis and never return. Ariadne and Hercules remain skeptical of Goran's newfound loyalty to them, noting how much quicker to trust Jason is than they. But for now, they must put their faith in Goran's word.
The group all returns to Atlantis and all the men in the army swear loyalty to Jason and Ariadne. Preparations are made for Jason and Ariadne to get the blessings of the gods the following morning. Ariadne admits to Jason that Atlantis doesn't feel like home the way it used to. Ariadne is feeling doubts because of what Pasiphae said but before she can share what exactly was stated, Jason says that Pasiphae is not to be trusted and Ariadne decides to put her doubts to rest. Meanwhile, Pasiphae is shown to have been resurrected through the powers of dark magic.
Pythagoras goes to Icarus and tells him about what has transpired, including everyone's return to the city and the fact that Jason and Ariadne will soon be on the throne. Pythagoras is preparing to lay a verbal smackdown on Icarus but before he can say anymore, he asks what happened to Daedalus whom is lying asleep, bloody and battered. Pythagoras then says how this is clearly why he betrayed him and Icarus learns how Pythagoras used his betrayal for their plan. They admit their feelings for each other but Pythagoras says he can never forgive Icarus for what he has done. Just as Pythagoras leaves, Daedalus wakes. He comforts his heart-broken son, understanding the hard place his son now finds himself but showing him compassion nonetheless.
Pasiphae re-appears in Atlantis and takes the storm with a new face scar and more angry vengeance in her sorcery than ever. She kills Goran because he refuses to swear loyalty to her and the remaining soldiers swear loyalty to her because they fear her wrath. The soldiers then strike before Jason and Ariadne can receive their blessing from the gods. A battle breaks out in the temple, and Melas ends up dead at the hands of Pasiphae while Cassandra runs off with Jason and the rest of our heroes. Yet again they must flee Atlantis, though they must hide until nightfall when they can make their escape. Fearing the worst, Ariadne asks Jason what happened between him and Medea. He admits that they had a moment during his darkest times but that whatever happened is over and he will never see her again. Icarus and Daedalus create a distraction to help our heroes get out of Atlantis, which consists of Icarus using some home-designed wings to fly overhead and drop bombs of fire-powder (basically gunpowder) onto the soldiers.
While most of the group is making their escape, Pythagoras goes chasing after Icarus since he sees he's about to get shot. He cradles his injured love, and then Hercules then comes to grab them so they can get back on track to flee the city. The following morning, Jason speak with Cassandra, who has had a vision of how Jason may defeat Pasiphae. It will be difficult, but not impossible. He must find the source of her power and destroy it. There's a golden fleece with unimaginable power in Colcous that he must retrieve on this quest. He must also get help from Medea to accomplish this all. All this would-be drama that we'll never get to see since the series has been cancelled!
Jason tells Hercules and Pythagoras of what he must do, saying there will never be peace until Pasiphae is defeated. He tells Ariadne next of what he must do. She wants to come with him and wants to know who will protect him from himself. He must go at it alone. Atlantis is being torn apart under Pasiphae's menacing rule while the group makes their way to the shore to set up camp. Cassandra has another vision of Jason aboard a ship called the "Argo" and being unfaithful to his Queen-wife. Again. Meanwhile, Medea is somehow in on this vision and learns of Jason's impending arrival. Which we will never see.
