츠나시·타쿠토는 청춘을 구가하기 위해 본토에서 헤험처 건너다 표류한다. 타쿠토는 스가타와 약혼자 와코에 의해 구조되고 남십자 학원 고등부에 입학하며 순조로운 청춘을 시작하지만 비밀조직 기라성 십자단에 의해 납치되는 와코를 발견하며 충돌하게 되는데...

기라성 십자단이 두려워하는 「은하 미소년」에게 패배한 기라성 십자단이었지만, 변화의 호기로 보고 은하 미소년을 넘어뜨린 사람이 조직의 리더가 되는 것으로 결정한다. 한편 타쿠토는 와코에 의해 남십자 학원·연극부 「야간 비행」에 소개되어지는데...

생활비가 곤란했던 타쿠토는 고교생이면서 세계적인 백만장 자의 아내 인 와타나베 카나코의 주선에 의해 그녀의 호화 여객선에서 아르바이트를하게된다.

한편 기라성 십자단의 총회에서 제4대 오토나 은행'의 대표는 사이바디의 소유권이 자신에게 있다고 주장하며 전투가 이루어지는데

도시를 돌아다니던 와코는 타쿠토와 조우하게되고 그와 시간을 보낸다. 그녀의 과거와 무녀로서의 의무에 대해 듣게되며 와코는 사이바디의 봉인을 유지하기 위해서 섬 바깥에 나올 수 없다는 것을 알된다. 타쿠토는 이에 그녀를 구할 수 있도록 기라성 십자단의 사이바디를 모두 파괴하는 것을 결의하는데...

학교 보건실의 간호사이자 키라보시 과학 길드의 탑인 프로페서 그린 교수 오카모토 미도리는 사랑의 묘약과 일시적으로 10 대로 돌아갈 수있는 특별한 능력을 통해 학교의 모든 사람들을 사로 잡지만 타쿠토의 마음을 사로 잡지 못한 채 제로 스페이스에서 그와 싸우게 되는데...

오늘은 스가타의 생일이지만 스가타는 자신의 생일을 혐오한다. 와코는 타쿠토에게 스가타 또한 사이바디를 소유하고 있다고 애기하지만 사이바디를 다루게되면 그의 목숨이 위험에 처하게 된다는 것을 알려준다. 생일을 축하하기 위해 스가타의 집으로 가는 중 그들은 기라보시 단의 공격을 받게 되고 스가타는 와코를 지키기 위해 힘을 꺼내게 되는데

Sugata remains unconscious much to Wako and Takuto's grief and the same glittering star member who attacked them in the previous night challenges Takuto on her Cybody.

Despite being happy that Sugata regained conscience, Takuto is angry at him for not accepting Wako's present. Just when they are at brink of fighting, Scarlet Kiss, the leader of one 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 license from his position as leader of glittering star's "Vanishing Age" squad and leaves another member, Marino You, aka Manticore in his place. Little 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 on Takuto brings forth the anger of one of Manticore's subordinates who decide to challenge him in in Zero Time.

Determined to bring revenge upon Kanako by taking over the 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.

Kanako is determined to become leader of the glittering star by defeating Tauburn in combat, but before challenging Takuto, she invites him to a date.

In order to confront Takuto once more and regain her position as a Star Driver, Benio volunteers herself to be a test subject in a experiment to reactivate destroyed Cybodies.

Having successfully managed to reactivate a broken Cybody, the Glittering Star uses the same process to repair Manticore's hoping to use its special ability to discover the identity of the West Maiden, but soon they find that maneuver 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 conforts her and finds that she is the West maiden, a fact that Glittering Star already knows.

Having captured Mizuno, the Glittering Star manages to break her seal and reach the Third Phase. While Mizuno manages to glimpse on 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.

Sugata and Takuto hang out with Wako to celebrate her birthday, but their cheerful day is disturbed by Kou Atari, another member of Glittering Star, who uses her powers on them to amuse herself.

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.