Apollon introduces himself as a Greek god. He helps Yui to her feet before placing his hand around Yui's waist and pulling her closer. After he kisses her on the cheek Yui pulls away, asking what he is doing. Apollon smiles and replies that he was being polite and introducing himself. When he sees Yui's expression he worries that he may have offended her and asks if they greet others differently where she comes from. Yui says yes and Apollon apologizes. Yui tells Apollon she was told to study with the gods here and teach them about humans but she wants to go home. She does not even know where she is. Apollon reassures her, saying that he is on her side and since he doesn't know where he is either, they can figure it out together.
Apollon whistles to summon Pegasus and asks for Yui's name. He comments that foreign names sound so beautiful before asking if he can call her 'Fairy' because she is lovely, just like a fairy. Yui and Apollon fly on Pegasus and are spotted by Balder, who looks displeased. From the sky, Yui and Apollon see that the entire place is an island. They return to the academy and Zeus welcomes them to his garden, his academy as his beloved students. The Japanese god of the sea, Susano'o, the Japanese god of the Moon, Tsukuyomi. The Norse god of light, Balder, god of fire, Loki, god of thunder, Thor. The Greek god of the underworld, Hades, god of fertility, Dionysus, and god of the sun, Apollon. Zeus has brought them here to learn about humans in order to revive the ancient link between the gods and humanity.
Loki asks if he really thinks they will do as he says and Takeru angrily demands that he and Tsukito be returned to their world. The two of them attack Zeus but are struck down by his lightning. Zeus says that if they use their powers indiscriminately, the academy will be destroyed. Therefore, he will seal their powers in limiters. Loki and Apollon try to remove their limiters but are unable to do so. Zeus tells the gods that these limiters seal their divine powers. No one can defy him here and the limiters are proof of that. When they earn the right to graduate, the limiters will remove themselves. Zeus shows them a large, round container which will be filled when they learn to understand the human heart. They have one year. If they cannot fill it within a year, they will be trapped here forever. When the gods complain Zeus tells them he will not entertain protests and calls for Thoth.
Thoth introduces himself as the Egyptian god of knowledge and Zeus creates many other spirits to act as classmates to the gods. He tells Yui her responsibility is to lead the gods to graduation. Thoth instructs them to gather in the auditorium tomorrow morning to prepare for the entrance ceremony in the afternoon and dismisses them, telling Yui to follow him. He says that Zeus modeled this academy after human schools. All necessary facilities have been provided and there's food in the cafeteria. Yui asks him isn't Zeus is being too willful, even for a god for suddenly bringing them here and that her parents must be worried. Thoth smiles and says he need not be concerned since at the end of the year, she will return to the time she came from through the powers of Chronos, god of time. When Yui replies that that is still no excuse for Zeus to do as he pleases, Thoth corners her against the wall and tells her Zeus has the future of the gods and humanity in mind. He says that eventually the sword she has will guide her way and to take care of it, not that she could remove it anyway. Thoth leads Yui to her room and tells her he will be in the library, come and see him if she needs anything before leaving.
In her room Yui finds a uniform and student handbook. She meets a doll, Melissa, who says he was created by Zeus to look after her. Melissa tells her he was made from clay, just like humans in many mythologies, but in his case there was a mistake. Nevertheless he likes his body since it is sturdy and mobile despite being a bit small. He tells Yui he is her upperclassman in this academy and she can talk to him when she is troubled. When she wants to cry, she can borrow his shoulder. Yui smiles and thanks him. She politely corrects him when he calls her 'Kutanagi'. Melissa replies that he knows, but continues to call her Kutanagi.
The Japanese gods are in their dorm and Takeru says he will find a way out of here. When Tsukito says they have to graduate he tells Tsukito not to listen to anything the old man says and pats Usamaro. In the Greek gods' dorm Apollon and Dionysus are in the hot spring. Dionysus asks Apollon if he intends to attend the academy. Apollon replies that regardless of his methods, don't they think studying humans sounds interesting? Dionysus comments that it seems like too much work to him and Hades agrees. The scene changes to the Norse gods' dorm where Balder is happily showing the tracksuit he had put on to Loki and Thor, declaring that it is fascinating. Thor comments to Loki that Balder seems to be fitting in well. Loki tells him that even if they are stuck in this garden, it doesn't change what they must do, to which Thor asks if that is their destiny as well. In her room, Yui lies on the bed and wonders how her family and friends are doing, and tells herself she will have to do this if she wants to return to her world before falling asleep.
The next morning, Yui wakes up refreshed and determined, telling Melissa that she is still uncertain about some things, but will start by doing what she can. Since she knows she can't get home herself, she must do this and asks Melissa to help her. Melissa happily replies that she is in expert hands. When Yui arrives at the auditorium it is empty but soon Balder arrives, falling down as he greets her. Yui tells him good morning too and Balder is happy that she remembered his name. Yui says she is relieved that he came because she thought no one else was coming. Balder replies that it is his first time attending school and he is excited. Then, his expression changes and he asks Yui if she has always been close to Apollon, since they were flying on Pegasus together yesterday. Yui tells him it was her first time meeting Apollon and he took her to see what kind of place this is. When he hears this, Balder smiles, placing his hand on Yui's cheek and says she met him first.
Apollon and Tsukito arrive at the auditorium and Apollon greets the two of them happily. The four of them wait near the stage but nobody else appeared to be coming. Apollon comments that don't the others understand, the only way out of this place is to graduate. Balder asks Yui what is done at an entrance ceremony. Apollon says that Thoth had mentioned it but he doesn't know and neither does Tsukito. Yui explains that the new students all assemble and it's a kind of celebration where everyone promises to study hard together. When she notices Tsukito taking notes about this she tells him there is no need to do so but he takes down her words as well. Balder frowns and wonders if an entrance ceremony is a contract ritual. Apollon asks if they will be met with a terrible curse if they break the promise and Tsukito asks if they will need a sacrifice. Yui hastily replies that it is nothing like that and it is not scary. Apollon suggests that they split up and convince everyone to attend the entrance ceremony with them.
Yui spots Takeru sitting under a tree and when she walks closer she sees that someone had drawn on his face while he was sleeping. Takeru glares at her when he wakes up and demands to know why she is staring at his face. Yui quickly uses her phone to show him his reflection. A shocked Takeru asks if she was the one who did this and Yui shakes her head. Loki reveals himself as the culprit, saying he loves to have fun before running away, causing Takeru to chase him. While looking for them Yui meets Hades but he tells her to stay away because being near him will bring her misery and walks away. The next person Yui tries to convince is Thor but he tells her if Loki isn't going then he doesn't need to either. Yui meets up with Apollon, Tsukito, Balder and Dionysus, who had decided to attend the entrance ceremony since Apollon insisted. Balder tells her they are running out of time so the five of them will prepare for the ceremony. The gods clean the auditorium and set up the chairs while Yui discusses their names with Thoth in the library.
The entrance ceremony begins with Thoth reading out the new students' names. Hades Aidoneus, Apollon Agana Belea, Yui Kusanagi, Takeru Totsuka, Tsukito Totsuka, Dionysus Thyrsos, Balder Hringhorni, Thor Megingyoruzu, and Loki Laevatein. Thoth then calls the student representative, Apollon, up to the stage to state the pledge. Yui notices that Apollon seems different as he stands in front of Zeus. Apollon says that as students, they enter the academy today. He is shocked by how sudden it was, bring brought to an unfamiliar place and not knowing what will happen next. However, there must be a reason for this. Over the next year, they will live not as gods, but as humans, studying their history, culture and love. With their wonderful new friends, they will all follow the academy's will and graduate. Apollon turns and pumps his fist in the air, telling everyone to do their best.
Yui thinks to herself that even though she had just met these gods, from now on they are going to spend the next year working towards graduation, living together. As Zeus walks past, Thoth comments that it has started, to which Zeus replies that everything begins now. They must weave the future, no matter what tragedy may arise.