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.

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.

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.

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.

"" 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.

Hikaru returns to the castle, but with her sword broken, she cannot call for her Rune-God. Meanwhile, Clef's group captures Alcyone and interrogates her. Clef, feeling something more behind Alcyone's words, becomes even more concerned. Suddenly, Bravada – the mobile fortress of Chizeta – arrives at Cephiro carrying the two princesses Tarta and Tatra.

Umi and Fuu head out to investigate without Hikaru, and encounter the guardian spirits of Chizeta. Aska from Fahren reappears in the skies above Cephiro for a rematch. Aska tries to prevent the Djinn from taking the two Rune-gods...

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…

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?

Umi, held captive by the mobile fortress Bravada, is forced into an outfit from Chizeta and then locked into a cage. The younger princess, Tarta, feels deep anger watching Umi, challenges Umi to a swordfight.

Fuu, held captive aboard the Dome of Fahren, is brought before Aska. Upon hearing that the Rune-God is alive, Aska begs Fuu for one of her own. Fuu gently declines, but Aska doesn't listen. Fuu suggests an archery match, saying that if Aska wins she can have her Rune-God, but if she wins, she must be returned to Cephiro.

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!

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.

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...

Umi and Fuu continue fighting the monsters in the castle's residential quarters. Hikaru chases after Nova, who had threatened to kill Lantis. Nova finds him with Eagle, and promptly attacks! Meanwhile, Umi and Fuu are struggling against the monsters, but they realize that the black sphere is taking in the children's fear to create monsters…

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!

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...

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 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?

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...