The spring has come since Yuichi reunited with Ayu, and everyone else's lives are back on track. However, when Mishio visits Makoto's birthplace, a miracle happens before her eyes.
Yuichi Aizawa comes to stay at his cousin's home in northern Japan after seven years. He meets Ayu Tsukimiya in the shopping district, who pulls him into running away from a taiyaki vendor with her.
Yuichi attends his first day at his new school, and later meets Shiori Misaka after another run-in with Ayu. The next day he finds Shiori visiting the schoolyard.
After his second day of classes, Makoto Sawatari tracks Yuichi down in the shopping district, trying to pick a fight. She collapses from hunger, however, and Akiko takes her in. The next day, after discovering some of her pranks, Yuichi suspects her of stealing his wallet.
Yuichi finds Mai Kawasumi in battle at night in the school building. Following an incident at lunch with a stray dog the next day, he joins her for lunch. After school, he joins Ayu in her search for a precious object, with no results. That night, he brings Mai some dinner.
Mai is implicated by the student council for some broken windows. Yuichi visits Mai again at night, but Makoto attracts the attention of the night watch. Makoto runs away from Akiko's house after a heated quarrel with Yuichi.
Yuichi searches for Makoto at night, and finds her in the shopping district. Shadowing her, he follows her to the hill overlooking the city and discovers that she found a stray cat. He takes both of them home, and the cat is named Piroshiki. Yuichi and Sayuri convince Mai to take part in the upcoming ball. Piro and Akiko fall ill, and Makoto and Ayu take care of them.
At first, Mai makes a good impression at the ball, but the lights are destroyed and Mai is again implicated. When Mai faces expulsion, Sayuri convinces the student council to reverse the punishment by agreeing to join the council. On Mai's birthday, Sayuri is injured by the monsters Mai hunts.
Mai resolves to end the fighting once and for all. As Mai and Yuichi fight the monsters together, Yuichi traces another fragment of his lost memory.
Yuichi learns about Shiori's condition and Kaori's silence. Prompted by Nayuki, Yuichi spends an entire day with Shiori, forging happy memories.
Makoto falls ill, and Yuichi discovers her true identity.
Yuichi and Ayu watch a movie together, and as they become closer, Nayuki is heartbroken. Ayu takes Yuichi to her school, but they make a startling discovery.
Yuichi remembers what happened to Ayu, seven years ago, as well as the thing she was searching for—a little angel doll. Nayuki, Kaori, and Jun help him unearth the doll. Akiko is hit by a car in a blizzard. Ayu, in order to let Yuichi use the doll, asks him to let her go as a final wish.
It is now spring, and Mai and Sayuri have graduated. Although Akiko is on the road to recovery, a rift still remains between Nayuki and Yuichi. On the day Yuichi is scheduled to leave and transfer to another school, Nayuki sees a familiar name tag at the hospital.