After defying a powerful man to protect a woman from sexual assault, Akira Kurusu finds himself with a criminal record for doing the right thing. The subsequent fallout causes him to move to Shibuya and attend Shujin Academy following his expulsion from his previous school. Shunned by the people around him, Akira is constantly reminded to lay low and get through the school year without disturbing the peace.

Unfortunately, his arrival in Shibuya is nothing short of strange and troublesome. Akira finds an undeletable app on his phone, unsure of when he had downloaded it. And on his way to school, he gets caught in the rain alongside Ryuuji Sakamoto, Shujin's notorious delinquent. When the phone app suddenly triggers itself, the two are transported into an eerie world infested with demonic creatures.

As they find themselves cornered by these shadow-like beings, an innate power awakens within Akira, allowing him to fight them off. Now armed with a "Persona," a manifestation of his personality, Akira works with Ryuuji to unravel the mystery behind this unfamiliar world.