The story starts with Sorata Suzuhara, an elementary student who is visiting the Parliament with his classmates and teacher on a field trip. He is listening to music with his earphones on when the teacher is explaining about the Parliament to them and he looks sleepy. It is implied that he is extremely smart, being awarded a prize but is not proud with it and aiming for a Nobel Prize Award. His friend also marvels at his knowledge on historical stuff and states that he is like a teacher. After that, they head to the assembly hall, which is the place where politicians fight with their discussions on political affairs, as seen on TV. Sorata saw a beautiful painting of him playing with nukos accompanied by his housemate's window with some beautiful patterns on it, but he cannot recall its name. Suddenly, a female voice, saying "stained glass", reminds Sorata about it. He turns around to find her but he did not see anyone around and thinks that he misheard it. Then, he heard a beautiful song and thought that it was the BGM of the Parliament’s assembly hall. Sorata’s classmate did not hear it and tells him that it’s from his earphones. But Sorata knows that it is not, and thinks that it is a ghost. He brushes it off since he does not believe in such abnormal things. The screen then turns into a scenery of greens and blacks out. Two lines then pop up, saying, "Sorata… I… with you again…"
After that, he is brought back to light. Sorata wakes up, finding himself at an unknown place. He looks around but he cannot find his classmates and teacher, instead he saw people wearing kimonos and western clothing all in grey colour. Sorata thinks that he is dreaming and some random guy bumped into him and yells at him for blocking the way. Sorata tries to stand up but he cannot move his body, not to mention stand, and is feeling cold. He calls for help but nobody helps him. Just then, a teenage girl with shoulder-length pink hair and a sailor uniform came and helped him.
She’s bad with communicating skills and refers to a guide-book sort of thing to communicate with others. She was the only one who lend him a helping hand, he tells her that he’s cold and might be feeling unwell, which causes him to be unable to stand. The girl offered to help him but they need to switch places first. She took him to some alley and collects some rubbish and papers. She hands out one of her hand and made a bonfire. Sorata thanked her, she thinks for a while and replies him with a welcome.
Later, after Sorata is feeling okay, she extinguishes the flame with a fire extinguisher. Sorata asks her about the place and the era they’re currently at. The girl replies that they’re at Tokyo and the current era is the Taisho Era. Sorata is extremely horrified, he cannot accept the fact that he time traveled back to the past. Sorata wants to go back home and starts babbling what should he do, he’s trapped in the past. The girl offers him to go with her to find his way back since she’s going on some journey onto a ship later. Sorata explains that he’s from far, far away, not exactly like the fairy tale far, far away but in the sense that he’s from the future, not tomorrow, not the day after tomorrow but way far in the future. Since this poor time slipped boy has nowhere to go, he decides to follow the girl and asks for her name. She thinks for a while but she cannot recall her name, because she got her head hit by a brick real hard and she didn’t get her named called for a long time. Sorata was shocked.
Before the ship arrives, the girl decides to go back home and wait for a while. Sorata asks for her age and immediately regrets it, since he thinks that she doesn’t even know her name, how will she know her age.
- Ah, I’m 17!
The girl replies that even if it's her, she still knows her age, because she’s been counting them everyday. Sorata’s like, "Is she waiting for me to tsukkomi what she said?" Sorata asks her where the ship is heading to and who’s boarding the ship. She replies, ‘Where will it head to? I’m excited!’ and ‘What kind of person will it be? I’m excited!’, and left Sorata speechless.
Later on, they see some sakura petals flying down. The strange girl immediately recognizes it as the sign of the ship coming and rushes towards a vast field. Sorata starts to lecture the strange girl, telling her not to follow strangers so easily which he realizes that he also did it himself. She doesn’t seem to listen to what Sorata is babbling and becomes very excited when she sees the ship. The ship is a huge sphere-like flying object. Sorata, the future boy was shocked and keeps denying the fact that it’s a hi-tech ship and says that it’s not stated in his holy textbook. The strange girl ignores his babble and drags him into the ship.
The inside of the ship is like a city, with trees and rivers. Sorata keeps thinking about what the ship is, and finally concludes that he’s in a UFO (Unidentified Flying Object). Since he only believes in scientifically proven things. And, suddenly, they’re attacked by 2 guys, namely Kakeru Yuiga and Akito Syukuri. They’re captured by vines manipulated by Kakeru, with Kakeru holding the strange girl and Akito holding Sorata who’s still thinking about sci-fi spaceships and aliens in his head. Sorata struggles and demands them to release both him and the strange girl. Since he can’t do anything, he calls him a UMA (Unidentified Mysterious Animal), pervert, molester and complains that Akito’s heavy.
Then someone shows up saying, ‘Stop right there, you idiots’. Mikoto Kuga expects to see Akito only so she’s surprised to see Kakeru here too. Kakeru explains that he’s only using the easiest method to understand the situation and asks Mikoto to see the strange girl carefully. Mikoto is still against the two guys using brute force and asks both of them to release the strange girl and Sorata at once. Kakeru listens to her and retreats his vines but Akito doesn’t want to listen to her. Mikoto demands to have Akito release Sorata. Akito questions Mikoto what will she do if he doesn’t listen to her. Just then, another heroine, Nanami Shiranui, shows up. She comments that Mikoto doesn’t need to use her powers and hurls a chick called a Hiyoko hearer towards Akito and Sorata. It lands directly on Sorata’s head, causing Akito to run away in fear. Heishi Otomaru and Masamune Tooya show up and the latter suggests to change places and formally introduce each other.
They move to the meeting room and did a head count. Apparently, 4 guys are not at the meeting room, namely Senri Ichinose, Ron Muroboshi, Itsuki Kagami, and Akito Syukuri. So the only ones present in the meeting room are Kakeru, Sakuya Nijou (Mikoto's childhood friend), the strange girl, Mikoto, Nanami, Masamune, and Heishi. Masamune asks about Sorata and the strange girl’s background and such. Sorata introduces himself and says that he’s from the future, like about 100 years in the future, at the Heisei Era. Everyone was shocked but they accept what he said unconditionally, except Mikoto who keeps rejecting the truth. Masamune agrees to let Sorata stay so that he can find his way back when they’re travelling around.
Mikoto turns to the strange girl and asks where she got her uniform from. Heishi’s hyperactive reaction causes Mikoto to ask someone to stuff his mouth with something. The uniform was supposedly handed over by an organization called ‘The World’ when they board the ship, not before boarding the ship. The strange girl tells them that she got hers from someone years ago, and she cannot remember who the person is because it’s been a long time since she last met the person. Sakuya believes her and suggests everyone to stop questioning her any further. Heishi agrees, since it’ll get more complicated and his puny brain cannot stand it which causes Nanami to call him Aho (阿呆, fool). The ship is already flying, so they cannot bring the two newcomers to the police station to solve things out and decide to just let them tag along. Sorata, who cannot accept the fact that the ship is flying, because he cannot see any propellers or engines, is continuously denying it. Mikoto stops him by telling him to stop whining. Sorata keeps murmuring to himself and eventually passes out.
Even in his dreams, Sorata is still saying that he doesn’t believe in magic whatsoever and thinks that manga, anime and games are stupid and hopes to wake up from this ‘dream’. The scene then changes to a room where the three girls are conversing. As a matter of fact, their ability is to protect world’s peace, and is given as a task by ‘The World’ organization. They’re going to travel to different countries like America, England, Germany, France, Russia, etc… though it’s still unknown where they’ll actually be sent to. That aside, they need to search for rooms for the strange girl and Sorata because they’re out of rooms. Mikoto refers to Sorata as Kobouzu and comments that since he’s a chibi he can basically sleep anywhere. Sorata who woke up a little bit earlier when Mikoto makes her comment jumps up and disapproves Mikoto on calling him ‘Chibi’. Mikoto asks him to sleep with Kakeru and Masamune who both share the same room for tonight which Sorata protests. He doesn’t want to sleep with someone who just attacked him during broad daylight. Nanami, who’s tired, asks the strange girl and Sorata to just go and sleep over at her place. But Nanami states that Sorata seems to be scared of Nanami, though he denies it. Mikoto sighs and ask Nanami to go over her place and let the strange girl and Sorata have Nanami’s room for tonight. She says that she’ll think of something tomorrow and asks Nanami to bear with it.
Just then Kakeru came in and offered to show the strange girl around tomorrow, and ask her to join his group. Since they’re the only humans at the ship, chores like cooking are done by themselves. They are divided into three groups and take turns to carry out the chores. For this week, Nanami’s team (Nanami, Akito, Ron and Heishi) are in-charge of preparing meals, Mikoto’s team (Mikoto, Sakuya and Itsuki) are having a rest and Kakeru’s team (Kakeru, Senri and Masamune) are in-charge of the second floor patrol. So, the strange girl is going to look around the ship with Kakeru and his teammates, what’s left is Sorata.
- Option 1: Have a look around the ship with the strange girl
Sorata decides to accompany the strange girl tomorrow which makes her happy. The next day, Kakeru brings the strange girl and Sorata to meet the other team members, Tooya Masamune and Ichinose Senri. They bump into Masamune and together, they head to Senri’s room. Kakeru knocks on Senri’s door, but Senri refuses, so Kakeru threatens to destroy his door.
Just then, the door cracks open with Senri hiding behind. Kakeru demands Senri to go to the rooftop with them, but Senri rejects. He notices that there are newcomers and Masamune introduces Sorata and the strange girl. Before the strange girl can finish her sentence, Senri shuts his door. Masamune rages at Senri while Kakeru once again threatens Senri to destroy his door. Masamune stops Kakeru and asks Senri to open his door.
- ???: Nice to… meet yo–
- Senri: *closes door*
- Masamune: Hey! Senri! It’s rude to do that! Open the door!
- Kakeru: Okay, let’s just destroy the door!
- Masamune: No! Don’t destroy the ship!
Just then, the ship shook. Akito arrives, panting and tells them to head to the canteen. Senri is still in his room and Akito demands him to come out. Since Senri doesn’t answer, Akito destroys Senri’s door and forces him out from his roon. After that, they rush to the canteen. When they arrive, Sorata notices that Mikoto is absent and the strange girl asks Sorata if he is fine even though she is shivering.
- Option 2: Go and search for a room with Mikoto
Sorata decides to search for a room to sleep in with Mikoto since he’s worried that Mikoto will end up finding some strange place for him to sleep at. The next day, Sorata meets up with Mikoto and her teammates, Sakuya and Itsuki. Sorata asks Mikoto to introduce Itsuki but she tells Sorata that Itsuki isn’t worth to be bothered. Since Mikoto isn’t going to introduce Itsuki, he self-intro himself and asks Sorata to help introduce him to the strange girl. Mikoto cuts in and tells them to continue to search for Sorata’s room.
They don’t have much luck in searching for a room for Sorata, so Sakuya suggests to have a fortune-telling session but Sorata declines. Sakuya ignores what Sorata said and starts to read Sorata’s fortune. He concludes that Sorata has a very good luck, everyday in this month will be a great day for him. Sorata rages at Sakuya, saying that the results is inaccurate. Sakuya marks that it’s disappointing to hear that his fortune-telling is inaccurate. So, he gives Sorata a riddle. "A warm animal that’s beside a fire." Sorata answers that it’s Hiyoko (Chick) and Sakuya asks for the reason. Sorata replies: Beside a fire -> Hi no Yoko [火の横（よこ）] -> HiYoKo (ヒヨコ)… and says that it’s only a gag. Sakuya congratulates him for getting the correct answer and tells him to continue to search for his room.
After awhile, Itsuki is bored with searching for Sorata’s room and suggests Sorata to just sleep outdoors, in which Sorata protests. Sorata notices an army of little chicks and decides to follow them. Mikoto and the two guys followed Sorata and they arrived at the Hiyokos’ room. Mikoto comments that the room is suitable for Sorata to live in. Sorata doesn’t want to live with the Hiyokos but he has no other option, unless he really wants to sleep outdoor Suddenly, the ship begins to shake. Mikoto decides to go to the rooftop to check what has happened. She instructs Sorata, Itsuki and Sakuya to go to the canteen because it’s safer over there. She warns them not to follow her and rushes to the rooftop. Since both Sorata and Sakuya are worried about Mikoto, Sakuya requests Sorata to follow Mikoto. So Sorata runs towards the rooftop to catch up with Mikoto.
- Option 3: Cook meals with Nanami
Sorata decides to prepare meals for the people in the ship with Nanami and her teammates. Nanami rejects Sorata’s offer to help out since she thinks that she already have enough people helping out. Sorata isn’t hurt by that, instead he’s like "Okay, then, I’ll just go with Mikoto to search for a place to sleep.’ Mikoto heard it and with Kakeru, they both insist Sorata to go and help Nanami. The next day, Sorata arrives at the canteen, only to be welcomed by one of the Hiyokos. He meets up with Nanami and her teammates. Sorata tries to recall Nanami’s name and Heishi’s name. He remembered the former:
- What’s his name again? Sorata thought.
- Heishi: It’s Otomaru Heishi! O.TO.MA.RU.HE.I.SHI!
- Sorata: … You don’t need to be so loud, I know it already.
- Heishi: Don't lie! Your face’s like ‘Who’s this guy??’ just now!
- Sorata decides to let it be since he thinks that he’s most probably smarter than Heishi.
- Heishi: This kid, he’s being stuffy just now.
Sorata then sees Akito and recalled about what happened yesterday, that he’s scared of birds. Akito notices it and says that he knows that Sorata’s looking down on him. Nanami introduces Akito by making up some silly origin of his name. Heishi marvels at Nanami’s quick thinking skills and decides to try it out by introducing their last teammate, Ron Muroboshi. Sorata sees Ron and thinks of him as the kind of guy who will appear at those ‘Beware of Suspicious Guys’ posters. Heishi thinks hard and repeated Ron’s name, but he failed to make up any. Sorata tells him that it’s okay and he’s pretty much remembered it already because Heishi repeated it for a number of times already. After introducing each other, a chef chick interrupts them in an angry tone. It wants them to go and whip up some food at the kitchen now or they’ll run out of time.
At the kitchen, Nanami and Heishi are preparing their breakfast in a really weird way. She prepares the fishes with her kunais and Heishi grilled the fishes by adding in a huge amount of sugar. Nanami suggests to Heishi to add some Miso Soup and some smashed lizard tails to add some hidden flavour into the dishes. Sorata’s yelling at them for making such weird dishes, are they cursing someone by adding lizard tails into the food. Akito cannot stand it and asks Nanami and Heishi to take care of what they did. He requests for Sorata’s help to whip up some food, and they succeed. The chick is happy with Akito’s work but Akito flinched at the sight of the Hiyokos. Suddenly, the ship shook real hard, as if it was hit by something. Everyone rushes out to the canteen. And according to Heishi, this isn’t the first time they got assaulted. They decide to stay at the canteen because only the upper part of the ship was attacked. Nanami realizes that Kakeru and company are at the upper part showing the strange girl around and Akito dashes out to head to where Kakeru and company are at. Nanami wants to follow them, but was stopped by Ron.