A boy named Takuto Tsunashi, swims from the mainland to a small island to make a difference in his life. After making friends with Sugata and Wako who rescued him, Takuto enrolls in the local school and gets himself involved in a conflict with the secret organization "Order of Glittering Star", who kidnap Wako as part of their plan to take control of the island's secret treasure.
The leaders of the many factions among Glittering Star decide that whoever defeats Takuto will become the order's main commander. Meanwhile, Takuto is introduced to Wako's friends at the drama club that also oppose the order's plans.
Takuto is short on cash and is invited by his classmate Kanako to take up a cleaning job at her own luxury cruise ship. Little does he know, that both Kanako and her employees are part of Glittering Star and one of them will become his next opponent.
While wandering alone through the city, Wako meets Takuto and the two spend some time talking about her past and her duties as a shrine maiden, until they find that they are trapped in an illusion created by one of the enemy's cybodies.
Professor Green, the school's nurse and leader of Glittering Star's science division is determined to infatuate all boys of the school with the aid of a powerful love potion and her special ability of returning temporarily to a teenager state. After failing to capture Takuto's heart, she fights it out with him in Zero Space.
It's Sugata's birthday today, and he hates it. Wako explains to Takuto why and tells him that Sugata also possesses a powerful Cybody, but Apprivoising it may put his life in danger. Whilst going to Sugata's home to celebrate his birthday, they're attacked by a mysterious Glittering Star member, and Sugata ends up doing what Wako feared most to protect them.
Despite being happy that Sugata regained conscience, Takuto is angry with him for not accepting Wako's present. Just when they are at brink of fighting, Scarlet Kiss, the leader of Glittering Star's "Filament" squad captures Sugata and uses his powers to increase the capabilites of her own Cybody in order to confront Takuto.
Head takes a break from his position as leader of Glittering Star's "Vanishing Age" squad and leaves another member, Marino You, aka Manticore in his place. Little do the order know that Marino's twin sister Mizuno is actually one of the four maidens.
Takuto and his classmates play a baseball game against Mizuno and Marino's class. During the match, Marino's growing interest in Takuto brings forth the anger of one of Manticore's subordinates who decides to challenge him in in Zero Time.
Determined to take revenge upon Kanako by taking over Glittering Star's leadership, her assistant Simone devises a plan to fight Takuto with the aid of Takashi who gains a second chance to confront Tauburn.
Having successfully managed to reactivate a broken Cybody, the members of Glittering Star use the same process to repair Manticore's cybody hoping to use its special ability to discover the identity of the West maiden. They soon they find that ploy to be a mistake when it escapes Marino's control and goes berserk.
Mizuno and Marino's estranged mother returns and a desperate Mizuno tries to leave the island to avoid her, but her maiden powers prevents her to do so. Wako confronts her and finds that she is the West maiden, a fact that already known by Glittering Star.
Having captured Mizuno, the members of Glittering Star manage to break her seal and reach the Third Phase. While Mizuno manages to glimpse Takuto's past and his days before he gains his mark, he struggles against Head, whose cybody resembles his own in both appearance and abilities.
Having assembled all remaining able pilots under his leadership, Head takes over Glittering Star and prepares for the breaking of the two final seals. But first they must defeat Takuto, who now must find a way to defeat his newest opponent, Madoka Kei, without bringing harm to her.
Takuto's room is destroyed by fireworks and Sugata offers a room at his mansion for him to stay. To make ends meet, Takuto starts working at the same karaoke bar as his classmate Keito Nichi, unaware that she is the East Maiden, and also a member of Glittering Star.
Ryousuke Katashiro, Head's second in command, reminisces about his past with his former fiancee Sora and Head. Meanwhile, Ginta Ryo, another member of Glittering Star, uses his First Phase ability to spy on the island's inhabitants and find out why Head is unwilling to break the final seals so soon. He decides to challenge Takuto by himself, but not before have him poisoned by a snake.
After Kou was defeated by Takuto once again, Madoka volunteers herself to an experiment to further increase her cybody's abilities, but in result her body was fused with it, leaving Takuto defenseless as he is unable to fight back without harming her.
The time has come for the drama club's play and Takuto's first performance. Along the spectators is Hana, an old friend of his who comes to meet him and Wako. After the play, Sugata allegedly falls into into a deep slumber again and finds that Keito has used her powers to keep him awake, discovering that she is the East Maiden.
The Vanishing Age squad is more determined than ever to break the seals and Takuto is forced to face three of their members at once. He manages to overcome them thanks to Sugata's help, but unbeknownst to him, Sugata himself is later introduced to the Glittering Star as their new leader.
The members of Glittering Star prepare themselves for the destruction of the remaining seals. After being pulled into Zero Time for their final battle, Takuto and Wako learn that Keito and Sugata are members of the Glittering Star, and when the Eastern seal is released, the King Cybody, Samekh, is finally broken free.
Reiji shows his true colors and uses the powers of his cybody to hijack Samekh and restore all cybodies Takuto defeated to put them under his control. The other members of Glittering Star regain control of ther cybodies and confront Samekh just to be easily overpowered by it, and it's up only to Takuto to put an end to his father's ambitions and rescue Sugata.