Naoya was the first student to talk to Kōichi on his first day of school, and became his friend soon after. He, along with the rest of the class, was hesitant about explaining the curse to Kōichi, though Naoya promised to explain things to Kōichi in June (which never happened).
In "Put Flesh", Naoya was scolded by Izumi for telling Kōichi unnecessary things about the curse and putting them all in danger, and both of them were arguing when Sanae Mizuno called Kōichi, and overheard her death.
In "Sphere Joint", after witnessing Mr. Kubodera's death, he called Kōichi, Yūya Mochizuki, and Izumi to meet for further discussion of the class 3 calamity.
After learning about Katsumi Matsunaga, they set off in "Hair Stand" to look for him, in the hopes they could replicate his method for halting the curse. During this time, they had fun at the beach while waiting for Matsunaga's return. Naoya organized a competition for lunch. He also picked the teams (pairing himself with the girls, Izumi and Takako), jokingly referring to Kōichi and Mei's team (along with an indignant Yūya) as "the nonexistent team." The results of the game were inconclusive, although Naoya managed to catch a bundle of kelp, which he promptly dropped on Izumi's head.
As the group was preparing to leave, Takako's beach ball blew back into the water. Naoya watched as Junta went to get it and was the first to notice when his classmate stopped moving. Naoya, along with Kōichi and Katsumi, rushed into the water, but were too late to rescue Junta, who was hit by a yacht and eviscerated.
In "Body Paint", Naoya appeared in Kōichi's guilt-driven dream. Later, he met up with Kōichi, Mei, and Yūya to look for the item that Katsumi left in the old classroom. There, they found an old tape recording and began to listen to it. However, they heard a teacher coming and ran to hide, in the process of which Naoya broke the tape. Yūya offered to help fix it, but explained it could take a while.
In "Body Paint", Naoya was among the students who went on the class trip, taking the group picture. By this point, Yūya had repaired the tape, and he, Naoya, and Kōichi listened to the repaired tape and learned how to break the curse: kill the Extra student.
At dinner that night, a tense atmosphere came to a head when Izumi stood up and accused Mei of being responsible for the curse, demanding that she apologize. Naoya took Mei's side and defended her, alongside Kōichi and Yūya.
Shortly after, Naoya barged into Mei's room in order to tell Kōichi he "might have done something terrible." He elaborates in "Makeup", explaining he thought Tomohiko was the dead student. To make sure, he started to interrogate him, and when Tomohiko didn't remember the things they used to do in their childhood, Naoya accused him of being the Extra. Tomohiko denied this, and in their argument, Naoya accidentally pushed Tomohiko out a window. Horrified and sure he'd killed his friend, Naoya had come looking for Kōichi, who assured him a fall from that height probably wouldn't be lethal. However, upon going to check on Tomohiko, they found he was gone.
Naoya later met with Yūya and started to look for Tomohiko, urging everyone to evacuate the building because of a fire. Instead, they met Keiko Numata, who'd already stabbed Manabu Maejima and assaulted Takako in her room, when they went looking for Ms. Mikami, and proceeded to attack them. Her knife falls and cuts Naoya in the leg, preventing him from walking, but Yūya was able to help him escape by dragging him out a window. After Yūya and Naoya escaped from Keiko, he opened an emergency door, only to find her waiting.
In "Stand by Oneself", Naoya was pushed out of a window by Yūya as Keiko continued to chase them. Before Yūya could follow, he was grabbed by Keiko, who tried to pull him back in and finish him. Naoya hurried to the rescue, inadvertently pulling Keiko out of the building and onto him as all three crashed to the ground. Keiko prepared to stab him when Tatsuji Chibiki came in the nick of time and turned her knife on her. Naoya and Yūya followed him to his car, where Mr. Chibiki treated Naoya's leg. A few minutes later, Tomohiko's body was brought out. Naoya screamed at his friend to wake up and broke down in tears upon realizing he was dead.
The anime ends with Naoya and Yūya putting a tape they recorded into the locker, just like where they found Katsumi's original one. Naoya's last lines of dialogue (from the tape) are instructions to Class 3-3, telling them how to break the curse but advising them to work things out as a group, "so you'll have no regrets."