The girls head to the castle where a girl, looking like Princess Emeraude is waiting for them. After mentioning Zagato's name, she goes berzerk, and climbs into her own machine. She starts to attack them, and they fly out of there (the girls are in their machines.) Once outside, they start to get into a battle with the machine, and get the truth from Princess Emeraude, saying it's her. She then tells them, how her sorta love affair (falling for Zagato actually) was a big no-no for the pillar who watched over Cephiro, and imprisioned herself so that feelings wouldn't get in the way. It was too late for that, and she reveals inorder to save their land, and fulfill her wish, they would have to kill her! She then reveals no one from Cephiro or suicide couldn't kill her, so that's why she summonded them. After attacking them, the girls combine into one machine, kill and proceeds to kill her. The huge light appears, and we see Princess Emeraude and Zagato together.

The girls start to head towards the flying mountain in the sky, and remembers the good times, and bad times they had. They then get a message from Princess Emeraude, telling them to grant her wish and save Cepiro. They finally reach the place, only to find Zagato in his own Machine preventing them to come any further. They fight, they get injured, and when it looks like they don't win, they combine all of their powers, Red Lighting, Dragon Water, and Green Gale. They shoot it towards Zagato, where it kills him. In the final scene Princess Emeraude screams in horor as Zagato is killed off.

During the fight with Regalia, Hikaru tries reaching out to Nova who disbelieves what everyone says about Debonair while the new allies help comfort people in the castle. Lantis is trapped inside the rogue Rune God...

Nova is now back in Hikaru's heart where she belongs. With her dying breath, Alcyone unveils Debonair's location: Cephiro's alternate realm. The Magic Knights and their Rune Gods are ready to end the struggle once and for all...

Ferio greets the three girls upon their return to the castle and explains that he is the younger brother of Princess Emeraude. The three girls are reunited with their old friends Caldina, Lafarga, and Ascot. They are introduced to Lantis, the younger brother of High Priest Zagato, who recently returned home from Autozam.

The Crown room allows but Hikaru and eagle to enter but who will be able to handle or touch the crown to determine the new Pillar?

Eagle, in combination with Geo's GTO, manages to break the barrier and enter Cephiro Castle. Inside, Alcyone responds to Debonair's call and allows the dark lady and her monsters to enter the castle! Selece and Windam attempt to block the GTO. Meanwhile Lantis heads for the top floor to confront Debonair at the crown room.

Eagle escapes from his cell and searches the castle for a way into the crown room. Since Eagle has biological data on Lantis, the intruder searchers for him and his sword. Eagle finds Lantis interrogating Alcyone and the two confront each other. Lantis sets to attack when Hikaru suddenly jumps into the battle! Meanwhile, Clef's rig and Lantis' sword start to glimmer...

Hikaru, Umi, and Fuu have been reunited with their families, but their hearts are still not at ease. The three promise to meet each other at Tokyo Tower, the place where they first met. Suddenly, with another mysterious flash of light, the three girls are whisked back to Cephiro, where Mokona and Clef await them.

Now that Cephiro has lost its Pillar, Princess Emeraude, it is under attack from three countries – Autozam, Chizeta, and Fahren! Clef doesn't want the girls to get involved in this new war, but Hikaru Umi, and Fuu agree to it on their own.

Hikaru and Lantis embarked on a journey in search of a new Pillar. Before them is a desolate wasteland so different from what Cephiro once looked like. In addition, the monsters that roam the land have grown in power. Eagle attacks the traveling pair and captures Hikaru. Lantis tries to follow, but Alcyone stands in his way!

Umi and Fuu, sensing Hikaru is in danger, get into their Run Gods and fly off. Meanwhile. Hikaru awakens from her dream with Nova realizing that she is aboard the Battleship NSX. She is taken to Eagle, where Eagle explains why Autozam is invading Cephiro.

Hikaru sits depressed, unable to help her two kidnapped friends. Seeing Hikaru so sad, Presea is determined to revive the broken sword. Nova appears in Hikau's heart and tells her that every hardship she has faced is all Emeraude's fault. Hikaru, attacked by Nova's words, slowly falls into the darkness within…

Ascot sends one of his worm creatures to kill the Magic Knights. Ascot decides to take a nap while his creature kills them. The girls gives Presea Escudo, along with their weapons. Presea proceeds to make them in another room, and the hear the monster. The girls tells Presea to take care of their weapons, while they handle the monster. The worm attacks the Magic Knights who are a bit sucessful in defending themselves, but it turns and heads for someone else... Presea! Weak, Presea finally completes their weapons, but the monster breaks into the room. The ceiling falls, and it hits Presea. The girls see Presea, and their new weapons (each of them have swords). They then use their new weapon to kill the monseter. They all rush to Presea who is at her last breath. She dies, and Hikaru sworns her revenge. Ascot wakes up from his nap and calls his creature only to find his remains killed by the Magic Knights. He swears he'll avenge his death as well.

Alcyone spies on Zagato, as he talks with Emeraude. She notices again, he is not physically attacking her, but merely just verbally making trouble. She slolwy gets more of her doubts with the ""kidnapping"" of Princess Emeraude. Mokona leads the girls into a hot (asui!) volcano where the last Machine is being held for Hikaru. Umi and Fuu starts to get worried about Hiakru when she acts weird, and is disappears (like the others did.) When this is all happening, Zagato manages to also get to the Volcano when Hikaru just went in. He strips Umi and Fuu's powers, just intime when Hikaru gets back. Hikaru and Zagato talk for a bit, and he takes her power also. They talk for a bit, for a little more, and he fires a fireball towards Umi and Fuu.

Late that night, Umi visits Clef, to apologize for originally not wanting to become a Magic Knight. Meanwhile, Fuu and Ferio were talking about Princess Emeraude and Hikaru awakes from a nightmare, and wanders sleeplessly around the castle. She finds Lantis comforting Mira. Suddenly, Autozam's battleship NSX appears above the Sephiro castle.

Hikaru, Umi, and Fuu ask Eagle why Autozam is invading Cephiro, when a giant metallic dragon appeared above them! It is Dome, the mobile fortress of Fahren, led by First Princess Aska, who wishes to become the Pillar of Cephiro. The girls follow Eagle's FTO which flew off to spy on Dome.

Nova skillfully confuses Hikaru her by distorting her memories of Umi and Fuu. Nova uses Hikaru's feelings towards Lantis to break Hikaru's determination. Hikaru's fears and doubts cause her to fall deeper into the darkness. Can Presea help her?

Aska tries to keep Fuu aboard the Dome, but Ferio jumps into the scene and rescues her! However, Hikaru's battle with Nova seems to be all but lost. Can Presea's desperate pleas to Hikaru reach the Magic Knight's heart?

Hikaru has returned after reviving Rayearth's sword, but doesn't remember confessing her love to Lantis! Hikaru later bumps into him in the castle garden en route to see Clef. Meanwhile, aboard the bridge of Autozam's battleship NSX, Eagle commands for the launch of the Laguna Cannon to see how Cephiro will react. The attack on Cephiro castle has finally begun!

Hikaru dreams of Cephiro from when it was peaceful. There, she sees the conversation between Lantis and Zagato, with princess Emeraude watching from behind the columns. Zagato asks Lantis about the Pillar system, and he answers...

Hikaru confesses her dreams concerning Nova and Debonair since she got back to Tokyo. Geo, worried by the loss of communication with Eagle, decides to attack. Just then, Aska's Dome reappears! Seeing that the Run-Gods are not out to battle, Aska thinks that Fuu has been defeated and calls giant Sang Yung to protect her!

The crown starts to change shape as Hikaru and Eagle both safely enter the crown room. But which will become the new Pillar of Cephiro? Just then, Tarta and Tatra of Chizeta arrive aboard the Bravada. Umi leaves Ascot to protect the castle and heads out. Tarta and Tatra challenge her to a personal duel. They tell Umi that if she wins they will stop their invasion of Cephiro...

Eagle having been captured breaks out and starts searching for Lantis with his bio info he can then access the crown room. Lantis continues to interrogate Alcyone when Eagle confronts Lantis then all of a sudden Hikaru jumps into the middle of it as well.

The girls run into what seems like to be a deserted village. They are captured in a net, and find out that the villagers were hiding from monsters, corrupting their land. A monster then shows up, forcing the villagers to go back into hiding. They get the monster's attention by hitting it after going after a little girl. The monster attack them (setting them free), and with Hikaru's magic, she defeats it. Umi is happy, and suggests to hurry to Eterna to get Escudo, but suddenly falls to the ground. Hikaru runs to Umi, only to be challege by Alcyone, who was the one who injured Umi with her Ice Arrows. Alcyone is confident on beating them, but Hikaru's anger only makes her stronger. In the midst of fighting, Umi slowly wakes up, and sees Hikaru battling for her sake. Umi turns to Mokona and wishes for magic, where Clef's voice, proceeds to give her (since she is ready for it.) Umi stands up, and casts a ""Water Dragon"" spell that blasts Alcyone, who retreats. Umi once again falls d