Aya first appeared in "Rough Sketch", where she talks with Kōichi Sakakibara. She, alongside Yukari, Tomohiko, Naoya, Yūya, Makoto, Noboru, and Ikuo, was among the students who enthusiastically welcomed their new classmate.
In "Put Flesh", Aya skipped class. Walking down the sidewalk, she met Kōichi and the two had a brief conversation. Suddenly, the wind picked up, and a large window pane almost fell on both students. Thinking quickly, Kōichi tackled Aya out of the way. Lying side by side on the sidewalk, a distraught Aya began to wail that she didn't want to die, much to Kōichi's confusion.
Aya eventually went back to school. In "Build Limbs", Kōichi returns to the empty classroom to see that the class had elected a new female class representative. Aya had received 2 votes to Izumi Akazawa's 24. Aya was in class at the end of "Face to Face", watching in horror with the rest of her classmates as Mr. Kubodera pulled a knife from his duffel bag and proceeded to stab himself. In "Sphere Joint," she and the others watched as he repeatedly stabbed himself with the knife and bled profusely across the classroom. She ran out of the classroom, screaming with the other students. Standing out in the hallway with her friends, Izumi tried to calm the traumatized Aya down.
In "Body Paint," Aya and Yumi went looking for Chibiki, when they met Kōichi and Naoya, as the boys were looking for Matsunaga's tape. Declining an offer to join them, the girls left. The Ayano's had decided the only way to protect themselves was to leave Yomiyama City, packing up their car for an extended trip, and several cartons in the front hallways for movers. Aya said goodbye to Yumi, promising to call her once she and her family were safe. It was the last conversation the two had.
Driving along a mountain road, the Ayano family had almost escaped when several loose rocks fell off the mountain, one landing directly on their car's windshield. Aya's father, who was driving, lost control of the car and plunged over the side of a precipice. The student gossip at the beginning of "Glass Eye" stated there were no survivors, suggesting that Aya and her parents were killed instantly or died in the hospital despite the efforts of the doctors trying to save them.