The year is 2148. Two years after the end of the original Fafner in the Azure TV series, Tatsumiya Island and its surviving residents have returned to some semblance of recovery. However, things have become desperate for our hero, Kazuki; nearly blind now, and partially crippled from his battles with the Festum two years earlier, he clings to the promise his fallen friend Soushi made to him to return to the island and set things right again. Kazuki's hopes flare when a lifeform is detected within an unmanned submarine that comes floating into Tatsumiya Bay one night, but the person aboard isn't Soushi; it is a mysterious boy named Misao Kurusu who may not be entirely human, and who claims to have been sent by Sōshi. With Misao's arrival, hostilities break out anew between the Human Army and the Festum, and the Fafner pilots are thrown into the most desperate battle of their lives - this time, with the fate of TWO races riding on their shoulders. (Source: Wikipedia)

Strange things are happening around the town of Suiten. The daughter of a priest begins to see strange visions, spirits have started to roam the mountains, and Tarou Komori is having unsettling dreams. Due to the trauma of being kidnapped 11 years ago, he has repressed most of the memories that could shed light on what really happened. But they return in his sleep, combined with encounters beyond the realm of dreams. As the supernatural and psychological collide, three children struggle to face their demons and repair the breach between the spiritual and corporeal worlds.

Yuuta Hoshitani enrolls in the prestigious Ayanagi Academy in hopes of finding the high school student who inspired him. The academy is well-known for producing exceptional musical talent, but students must first compete for acceptance into the Musical Department. At the top of the department is the Kao Council—a group of third-year students who possess a great deal of influence over the school and admission into the department. The fastest route to entering the department for Hoshitani is to find a way into a Star Team, which would allow him to be taught by a member of the Kao Council. After catching the eyes of Itsuki Ootori, Hoshitani finds himself under the tutelage of the Kao Council's most eccentric member. Alongside him on Team Ootori is his roommate, Tooru Nayuki, fledgling Kabuki actor Kakeru Tengenji, the quiet Shuu Kuga, and Kaito Tsukigami, the younger brother of famous Ayanagi alumni Haruto. As Hoshitani struggles with his lack of talent, his teammates must also overcome their shortcomings. Facing opposition from other talented Star Teams, including the other four members of the Kao Council, Team Ootori must carve their own path as they aim to perform in the Ayanagi Festival.

After a successful Ayanagi Festival, Yuuta Hoshitani and the members of Team Ootori celebrate the beginning of a new year and their final semester as first years at Ayanagi Academy. However, with Itsuki Ootori expelled from the Kao Council, Team Ootori no longer qualifies as a Star Team. Stripped of their privileges, they also will not be allowed to participate in the upcoming graduation ceremony. Desperate to get their mentor back, Hoshitani and the others hatch a plan to convince the Kao Council to allow Ootori to reassume his former position.