The game opens on September 11, 2018. When Hayato is about to test his "Dragon Unit" flight pack on the school's roof, a girl falls from the sky, wearing a similar device. He tries to save her, but falls to his death; after this, he is transported back in time without any memory of the event, and manages to save her. Her name turns out to be Arika Tokitou. Ryuusei Academy and the Second Science Club prepare for a school festival that is scheduled for a month later, when Hayato's science professor, Genkuro Kanbara, gives him a smartphone chip composed of an "Agastia Stone", which theoretically would allow him to receive voice messages from the future. He installs it and does receive messages from the future, but is unable to tell what they are saying.
At one point, due to an accident with the Dragon Unit, Hayato's house blows up, forcing him to sleep in the science clubroom. He and the rest of the club decide that for the festival, they should put on a live performance for Hikari. During the month, Hayato and Hikari get closer, and he moves in with her. He helps her overcome issues with self confidence and to succeed at the live performance, and they become a couple. At the end of the festival, time moves backwards to September 11 again; the same month loops several times, with Hayato being unaware of it and having no memory of past loops. During each loop, he gets closely involved with one of the game's female characters, helps them with the festival, and with resolving their personal problems. While Arika is distant at first, she starts to lighten up to Hayato the more loops he goes through.
After going through several loops, Hayato returns to September 11 with his memories intact, and realizes that Arika is the only one who appears to have a connection to the looping. He confronts her, and while she admits to have a connection, she does not trust him to help her. When Hayato realizes that his house is about to explode, with Hikari and Arika inside, he gets them out instead of saving the Dragon Unit; this earns him Arika's trust, and she tells him that she is a time traveler from 2040. Learning that her presence caused a time loop, she wanted to return to her time, but was unable to as her time machine had broken. Hayato gathers parts to repair it with, and again gets close to Hikari. He learns that Arika's true identity is Akari Hino, and that she is Hayato and Hikari's daughter from the future. In the future, Hayato had become a workaholic, building a time machine while neglecting Hikari and Akira; in anger, Akira had stolen the time machine and traveled to 2018. As the time machine only works in a zero-gravity environment, they combine it with the Dragon Unit and take it to the 1,200 feet Sky Tower; their way there is hindered by an earthquake, but they are able to reach it with the help of Hikari, Tamaki, Yuzu, Nanari, and professor Kanbara.
The sender of the voice messages from the future is revealed to be the Hayato of 2040; as the future versions of Hayato and Hikari had seen Akari in 2018, they knew that they needed to recreate the events in order to avoid a time paradox that would cause Akari to cease existing. Because of this, Hayato had spent all of his time on creating a time machine by 2040, while he acted cold to Akari on purpose to give her incentive to travel back in time. The Hayato of 2040 then sent voice messages to his 2018 self to offer guidance and to cause an ontological paradox, ensuring Akari's continued existence. Akari travels back to 2040, breaking the loop, and makes up with her parents.