The narrative picks up with the protagonist, Natsumi, experiencing a "reset" and finding herself back in her room on the day of the school entrance ceremony, indicating the start of another loop. She quickly connects with Ando and W. Swan (Shiratori-sensei) via a messaging app, confirming the reset and the formation of their group.
In this new loop, Natsumi takes on the role of class representative, a position Ando usually held. She has been provided with extensive information by Ando and Shiratori-sensei to facilitate this. Shiratori-sensei refers to this loop as a "bonus stage" and exhibits an unusually forward romantic interest in Ando, much to the surprise of their classmates. Natsumi also intervenes to prevent Matsusaka and Kakimoto from engaging in the resale of game software and tickets.
Natsumi then visits Yuzawa to discuss her plans for this loop. Yuzawa is preparing for a debut in the entertainment industry and also for preventing doping in sports. Natsumi intends to help Yuzawa with her summer homework by using her own memories of past loops as a "past paper" strategy.
A significant development occurs when Natsumi reveals the loop phenomenon to her parents. Using her knowledge of past day trading, she provides detailed information that convinces them. Her parents are supportive, with her father offering financial assistance and her mother enthusiastically supporting Natsumi's initiatives, including addressing the doping issue by donating to the tournament organizers and promoting anti-drug abuse campaigns. Kakimoto, meanwhile, is offered a trip to Dubai by his parents.
Natsumi also encounters Kira, a musician, and impresses him with her musical composition, "Song for Tomorrow Morning." It is revealed that Shiratori-sensei is the original composer of this song, and Natsumi has received her permission to use it. Shiratori-sensei explains her reluctance to be in the spotlight in previous loops, citing potential negative perceptions of a teacher being a professional songwriter.
Later, Natsumi, Yuzawa, and Narumi go on a day trip to a hot spring. They encounter Sasahara, who has manipulated the hot spring's gender signs, causing a humorous "happenstance." During lunch, Yuzawa and Narumi remark that Natsumi resembles someone they know, but cannot recall who it is. They are also accosted by some men, whom Natsumi recognizes from previous loops.
The narrative then shifts to Kakimoto, who, feeling despair about the future, embarks on a solo journey to politically unstable foreign countries using his parents' credit card and forged documents. He faces hardship and finds himself in a desolate region, reflecting on the futility of his actions and the potential for the loop to end without reset. He encounters an elderly woman who offers him food and shelter, and they discuss the impact of conflict and the slow pace of recovery.
Meanwhile, Natsumi's parents, through their company Azalea Group, are involved in refugee relief efforts and have facilitated peace talks between warring factions. They are aware of Natsumi's involvement and her unique abilities.
Kakimoto is eventually captured by soldiers who intend to use him as a scapegoat to condemn Japan's involvement in the region's reconstruction. However, before he can be executed, a helicopter intervenes, implying external assistance.
The story then jumps to a later point in the loop, where the class discusses the concept of "Sage Mode," referring to a state of calm reflection after experiencing the loops. They acknowledge the significant impact Natsumi has had on their current reality, with her scientific advancements and the Azalea Group's influence.
The narrative also introduces a science fiction story written by Sasahara, titled "Paradoxical Chaos," which seems to mirror their experiences. The story features characters named Lance and Natsumi, who are siblings living in a war-torn future. Natsumi in the story is identified as a "compatible person" with a mysterious "Crystal Chaos."
The story then returns to Natsumi and Ando, discussing the advanced technology of their era, which has been influenced by Natsumi's actions. Ando expresses his admiration for Natsumi, both as a teacher and as the person behind these advancements.
The class continues to engage with advanced scientific concepts, including time-space control theory, and interacts with astronauts on a Jupiter orbital station. Natsumi's parents are shown to be actively involved in global initiatives, with Azalea Group playing a significant role in refugee aid and the development of new energy technologies.
The story highlights the close relationship between Natsumi and Ando, with Natsumi making Ando's favorite fried chicken and them sharing meals. The class also discusses the evolution of communication tools and the concept of memory transfer.
Later, Natsumi's parents express concern about her financial expenditures, but Natsumi explains that Azalea Group is restructuring and focusing on research, with new ventures like "Wiseman Industries" poised for growth. She also mentions her continued study of astrology and its connection to future development.
The narrative concludes with a glimpse into the class's daily lives, their interactions, and the ongoing impact of Natsumi's actions on their reality, including the development of new technologies and the continued growth of their influence. The story emphasizes the class's collective "Sage Mode" and their acceptance of the extraordinary circumstances they find themselves in.
