Set after the time of Sakura Taisen 4 (game), Kanzaki Sumire, during a training session was noticed that her spirit power (rei-ryoku) has dropped tremendously, below levels required to pilot the Koubu-nishiki. She decides to retire from the Kageki-dan while she still holds the position of "top star" in the dai-teikoku gekijyou.

In the future humankind has expanded and colonized other planets. Then an alien species, Victim, attacks the human colonies leaving only one planet, Zion. In an effort to stop Victim from destroying the last planet a training school, GOA, is set up to gather boys from the Zion colonies and train them to become pilots of the Ingrids AKA The Goddesses, five fighting robots that protect Zion. The boys must possess a rare blood type, EO, as well as a special ability, or EX. Zero (Candidate 88) has just arrived in GOA when he falls into the cockpit of the Ingrid Eeva-Leena. Since the synch between pilot and Ingrid are very sensitive everyone believes the Goddess will kill Zero in an attempt to synch. Just before Zero passes out he makes a full synch with the Goddess. Before he can find out more about the incident, his pilot training begins.

There are two kinds of people in the world, normal and psychics. Psychics are rare, powerful and feared. Burn Griffith met and befriended one of them, Keith Evans, two years ago. Now he has been looking for his friend, but when he finally succeeds, something's not right. The world has changed, and so has Keith.

Takane Takamine is great at everything she does, and her magnetic personality makes her the envy of everyone. She gets good grades, excels at sports, and even manages to become student council president during her first year of high school. But Takamine has a secret—she possesses an ability called "Eternal Virgin Road," allowing her to redo past actions and achieve a different result. While this might seem like a decent skill to have, Takamine must pay a price to activate it: she has to strip off a piece of her lingerie. After getting an imperfect score on a test, Takamine begins to remove her underwear during class and is spotted by her average and weak-willed classmate Koushi Shirota, who is bewildered by the sight. However, the very next instant, things reset and Takamine's test is now perfect. When Shirota decides to confront Takamine about her previous test score, she reveals her ability to him and blackmails him into becoming her "closet," making him carry around extra lingerie and put them on her. Her goal is to be able to use Eternal Virgin Road as much as possible in order to stay at the top of the school hierarchy. Left with little choice in the matter, Shirota accepts, starting an oddly intimate type of relationship with the most popular girl at school.