The following contains spoilers for Season 2, Episode 12 of Science Fell in Love, So I Tried to Prove It, now streaming on Crunchyroll.
Science Fell in Love's second season focuses on more than the Shinya/Ayame romance at Saitama University. This season also explores Kanade Kotonoha's own troubled love life, and in recent episodes, it seemed she had a good thing going with Naoya. However, Naoya's charming exterior is abruptly revealed to be a total sham.
In the end, as Episode 12 proves, Naoya and Kanade have no chemistry together after all, and not just because of Naoya's disturbing sense of entitlement when it comes to romance. He is a fearsome yandere who thinks he can force his own version of normalcy on Kanade, but he is completely wrong -- and it's up to Shinya to prove it.
In Episode 12, Naoya continues to pressure Kanade to accept him as her lover during Saitama University's festival, unafraid to show his grotesque yandere side. Naoya feels desperate to get Kanade to accept him, and with his sense of entitlement, he cannot take no for an answer. Kanade's rejection takes them both by surprise, and Naoya reacts in true yandere fashion; he quickly pushes things to new extremes, and Kanade is unprepared. Unable to handle Kanade's rejection, Naoya produces a Taser and knocks Kanade out. Kanade awakens in a dim warehouse, her wrists and ankles bound with rope.
In the warehouse, Naoya, while surrounded by several thuggish friends, explains himself. He tries to establish common ground with Kanade by outlining how he often faced rejection for being strange or failing to meet expectations, to the point where his father regularly beat him until he ended up in an orphanage. These experiences, according to the flashback, led Naoya to desperation, and he urgently seeks to get his ideal "normal" romance, even if he has to do so by force.
Like Kanade, he urgently wants to live the "normal" way, except he resorts to criminal extremes to do so, and even when the cool-headed Yukimura Shinya finds and confronts him, Naoya refuses to back down or reconsider his actions. In the end, the police arrive and arrest Naoya and his friends. Most likely, Naoya will never appear in the story again even if Science Fell in Love gets a third season. This show has a forgiving and optimistic tone for the most part, but there's no forgiving Naoya.
Episode 12 wraps up the season with an important message wrapped in a grim package. In this episode, Science Fell in Love dives deeper into the confusing and subjective field of what "normal" is in the context of modern Japanese society, and the conclusion favors Kanade over Naoya. Normalcy is about accepting others for who and what they are and embracing this as a tolerable or even lovable reality. Kanade once suffered from constant bullying due to her quirky ways, which led her to pursue normalcy at all costs, but there is no need for that now. Self-authenticity is Kanade's route to happiness, and there is no substitute.
By contrast, Naoya pursues normalcy in terrible ways, and unlike Kanade, he projects his insecurities onto others. He and Kanade have the same starting point of feeling insecure about being different, but most importantly, Kanade tries to be normal to keep others happy while Naoya tries to change other people for his own sake.
The yandere Naoya thinks he can force a normal romance by reshaping his partner and correcting their behavior, but not only are his methods brutal, but his goal is unacceptable as well. No one has the right to change someone else to fit any definition of "normal," but the entitled Naoya thinks he can. He's wrong. However, now that he's been outed and arrested as a criminal, he cannot attempt to force his own twisted idea of normalcy onto anyone else.