Three best friends, Hikaru, Umi, and Fuu, face being separated after their junior high school graduation. Under a cherry tree, rumored to hold a magical fairy, the three make a wish to stay together no matter what happens. 

Mokona, the fairy of the tree, hears their wish, and feels they are worthy of having it granted. Mokona reappears, and Hikaru meets the fire deity Lexus, who grants her a red ovum gem and allows her to see Clef, a rogue priest who can help Hikaru and her friends.

Alcyone, a supporter of Cefiro, begins to attack the city. Clef uses a magic spell to trap all the people of the earth into an alternate dimension for their protection. The three girls are the only ones to remain.

Clef joins Hikaru, Umi, and Fuu, and tries to protect them from Alycone's attacks. Hikaru is left behind, and as she is falling, Lexus comes to her aid. Hikaru accepts the responsibility of becoming a martyr, and she and Lexus head to fight Alcyone.

After an intense battle, Hikaru destroys Alcyone's deity. A portal has been opened into another world, and the castle of Cefiro begins to land on the earth. Hikaru sacrifices herself in an attempt to destroy it, but her attack is reflected back to herself by another deity.

Umi and Fuu stand outside the part of the city that had just become a battlefield. They cry and hope Hikaru is alive. At the same time, Lantis finds Hikaru alive. He protects her from Alcyone's final attack.

Fuu stands outside, looking at the empty city. She reflects on the battle, and wishes that she could have fought as bravely as Hikaru, to help her. Mokona comes to her side to comfort her.

Umi is inside an office building that she, Fuu, and Clef were hiding out in. She wishes Clef were awake so she could ask him to explain what was happening. Fuu enters, bringing food she found in the freezer of a restaurant. Umi sees Fuu is covering her hand with a glove, and gets angry when she finds that Fuu has received the green ovum gem.

After a long argument, Fuu leaves, so that she may be tested to find her deity. Clef wakes up after hearing the argument, but he and Umi are too late to catch Fuu. She leaves on a computer run train. 

Ferio sends Ascot off to get rid of Clef and Umi, and he follows Fuu. Afraid to battle, Fuu transports herself into her neighborhood. Ferio follows her, and begins to attack once again. Windam, the sky deity who gave Fuu the ovum, tells her to find him. Fuu hears a heartbeat and follows it.

Ascot fills the office building Umi and Clef were in with acidic bubbles that destroy anything they touch. Clef uses his magic to move himself and Umi to another building. Ascot finds them here, and Clef sends Umi off on her own, and is crushed underneath the building. 

Hikaru awakens. Lantis questions her about why she choose to accept the deity. Unsatisfied with the course of destiny, he traps Hikaru in a labyrinth that she may only escape from once she revives Lexus. While she is wandering through the labyrinth, Eagle destroys Alcyone for failing to complete her mission.

Umi runs from Ascot, who comes after her. She hears the voice of Ceres, but because she is afraid and arrogant, it cannot help her. Umi remembers why she became friends with Hikaru and Fuu. She receives the blue ovum, and the deity Ceres. In turn she begins to battle Ascot.

Fuu follows the heartbeat into the stadium, where she awakens Windam. They fly away to an airport, so that Fuu may battle in an open area and not destroy anything.

Hikaru is stuck watching her friends get beat from within the labyrinth. Lantis gives her a final chance. He asks her to find whether or not Umi and Fuu's battles have meaning. Hikaru realizes that Umi and Fuu are fighting for her sake. 

The final part of the trilogy opens up with a flashback of Emeraude and Zagato meeting under a tree. The scene changes to Lantis running, recalling an argument he had with Zagato. A ceremony is taking place, in which Zagato kills himself in the hopes he can fix the mistake he made.

Back in the present, Umi and Fuu are struggling to defeat Ascot and Ferio. Ferio finally seems to have given up, after a final, strong attack from Fuu. Ascot, on the other hand, keeps regenerating after each attack. Lantis is nearby watching, and he explains to Ferio that Ascot has been manipulated and taken over. Hikaru, after finally reviving her deity, joins her friends in the fight.

Once Ascot is defeated, Eagle transports the girls into the castle of Cefiro, where he robs them of their deities. Before Eagle has time to destroy the girls, they end up in another part of the castle. Hikaru watches Princess Emeraude, as she sings to Zagato, sitting very stiffly in a chair. The girls then realize that Princess Emeraude is trapped within her own mind, where she still believes Zagato is alive.

Lantis rescues the girls from Eagle, and sends them away while he tries to hold Eagle off from finding them. As a final request, he asks the girls to help save the soul of his brother Zagato.

Ferio, after realizing how he too had been tricked by Eagle, stays to help Lantis fend off Eagle. Extremely weak, Lantis gives his life to the power of his sword, which he entrusts to Umi, Fuu, and Hikaru. The three friends have summoned their deities, and are busy fighting Eagle. Even with all of their powers combined and the aid of Lantis's sword, Eagle keeps reviving the dead deity that was once Zagato's.

But Princess Emeraude, after feeling the immense power the girls had, awakens from her dream world and tells Eagle to stop. Emeraude, Eagle, Clef, and Ferio return home to rebuild the place they destroyed. Lexus, Ceres, and Windam leave Hikaru, Umi, and Fuu.

The trilogy ends with the girls graduating, and each leaving to go their own way from under the cherry tree.