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 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…

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.

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.

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?

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.

After battling a fierce monster, the girls find out that Mokona is able to project the land of Cephiro. They soon find out that they need to head for the skies for the other Machine, as well as their location (where they are currently at.) Soon after a bright light showed up, kidnapping Umi and Fuu. A picture of Clef (projected by Mokona's jewel) shows up and tells how there are unusual monsters, and other unimportant stuff and some back story that could be just brushed off. Hikaru remembers the map, and Mokona projects it. She heads towards Umi and Fuu's way and manages to get cut along the way due to some thorns. Mokona catches up with her, and notices the blood. Soon after the light is after Hikaru, but Mokona pushes Hikaru out of the way and in he goes into the light, while Hikaru falls into a ravine sort-like place. Hikaru tries to climb up, falls down, and manages to get hit in the head by rocks. She slowly figure out of the light monster work, and remembers that

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 and company head out to survey the NSX, but before them stands Alcyone! Hikaru, amidst the attacks from Alcyone, tries to convince her to fight along side them, but suddenly a change befalls Alcyone! She beings talking with an eerie voice that Hikaru has heard in her nightmares!

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.

The deterioration of Cephiro gains peed, and the girls must find a new Pillar soon. When about the qualifications for someone to become the Pillar, Clef shows the girls Princess Emeraude's crown. He tells them that only the one worthy of becoming the Pillar can touch the crown.

"" am Nova, the one that will kill Hikaru..."" Hikaru defends herself against Nova who ruthlessly attacks. Umi and Fuu arrive, but the three Rune-Gods are dragged into an alternative dimension created by Nova. Debonair appears to the three girls.