In the wake of their first home burning down, Nasa and Tsukasa Yuzaki are seeking temporary shelter at the Arisugawas' bathhouse. Though they have only been married for a short time, their relationship has only become sweeter by the day. Nasa is determined to spend as much time with his wife as possible, basking in the happiness of their marriage. The newlyweds find new ways to explore their relationship. From adopting a cat, going to an amusement park, and even watching an impromptu romantic comedy featuring Nasa's former teacher, every day is a new experience. But while Tsukasa continues to meet the people in Nasa's life, Nasa has yet to meet more of Tsukasa's family. Though they appear to be the picture-perfect couple to everyone around them, Nasa begins to wonder if he will ever learn more about his wife's mysterious past.

On her way to school one day, Suzume Iwato stumbles upon Souta Munakata, a young man searching for abandoned areas. The high school girl directs Souta to a nearby ruin, but out of pure curiosity, she herself decides to head to the same destination. Once there, Suzume discovers an isolated door with a dreamlike universe lying beyond it—a place that she can see and feel, but not enter. A strange stone rests on the ground nearby, but it turns into a cat-like creature and scurries away when Suzume lifts it. Suddenly afraid, she heads back toward her school, not realizing that her act of leaving the door open will have consequences. With the "keystone" released, the evil within the other universe can now freely escape and wreak havoc throughout Japan. Intending to correct her dangerous mistake, Suzume joins Souta—whose true goal is to prevent evil from festering—in finding and locking all open doors before the country is destroyed.

Impressed by Nanao Hibiya's skill with a sword, Kimberly Magic Academy instructor Theodore McFarlane saves the samurai from certain death amid a fierce battle. With his encouragement, Nanao enrolls in the academy, where she instantly becomes a celebrity after she and four of her peers save a student from an enraged troll. Under the leadership of Oliver Horn, a young man who seems to hide a troubled past, Nanao and her newfound friends start their magical apprenticeship at Kimberly—where only four out of five students make it to graduation in one piece. It does not take long for Oliver and his friends to experience the dangers of the academy firsthand, as a near-death encounter in the labyrinth under the school leaves Nanao grappling with her bloody past. The inexperienced yet determined students must stick together if they want to have a chance to survive and uncover the mysteries that the academy holds.

With the Interhigh Championship finally over, Seirin's basketball team refocuses their efforts, training harder than ever to get the chance to participate in the Winter Cup. Both Kuroko and Kagami see old friends walk back into their lives, providing a challenge both on and off the court. As new skills are developed and new alliances created, enemies from various teams—giants of high school basketball such as Yousen, Shuutoku and Touou—stand in the way of Seirin's steadfast attempts to get to the top. All of these schools prove to be formidable foes whose abilities progress exponentially, while Kuroko struggles to find a balance between his resolve to play as part of a team and his desire to win. With old wounds reopening, new challenges to face on the court, and a new set of foes—the "Uncrowned Kings"—vowing to defeat the new hopefuls, will Seirin ever be able to achieve their dream of beating the Generation of Miracles? [Written by MAL Rewrite]