During an escape from Sae's Casino in the Metaverse, Joker was attacked by a masked assailant. The assailant unmasks himself as Nagisa, who proceeds to shoot him. Nagisa then awakens from his bed, revealing it to be a dream. While sleeping in class at Kokatsu Academy, Nagisa is drawn into the Velvet Room, taking the form of a tunnel submerged in a sea, and it is occupied by Igor and his assistant, Merope. Igor cites Nagisa's knowledge of
choice as his reason for bringing him to the Velvet Room. Nagisa wakes up in the classroom and begins to see weird experiences around him that lead him to lose desire, such as asking two students from blocking the stairs, or helping someone who has just jumped off from a building. On his way home from school, Nagisa notices a weird app installed on his phone and encounters a talking owl, Lufel. Nagisa accidentally taps the app and brings himself and Lufel to the Metaverse, a supernatural realm representing the unconscious desires of humanity. Lufel explains that humanity's hopes and desires are being stolen, including Nagisa's. While attempting to leave the Metaverse, the pair are attacked by Shadows, creatures formed from warped desires who attack humans on sight. Nagisa awakens his Persona,
Jánošík, and is able to defeat the shadows with Lufel's help, allowing them to return to the real world. Realizing his potential, Lufel recruits Nagisa to help him reclaim the desire of the masses. Lufel points out to Nagisa a former baseball player, Takeyuki Kiuchi, who intentionally
rams into women in the subway, and says that in order to stop him, they must enter Kiuchi's Palace within the Metaverse and steal his treasure, an object which is the source of warped desires. On his way to school the following day, Nagisa meets with his classmate Motoha Arai and her best friend, Tomoko Noge, who aspires to play baseball professionally after Motoha abruptly quit baseball. Tomoko saves Motoha from being rammed by Kiuchi, but she herself is thrown onto the tracks, causing a career-ending injury that prevents her from playing baseball. Nagisa and Lufel enter Kiuchi's palace and discover that Motoha has also accidentally entered the palace, who awakens to her Persona after being physically and verbally berated by a Shadow form of Kiuchi. While traversing through Kiuchi's palace, they discover that Motoha hitting a
slider thrown by a Kiuchi, along with a scandal resulting from Kiuchi's purchasing of an
escort, forced him off the baseball team and into an office job, leading to his misogynistic desires. Nagisa, Lufel, and Motoha are able to defeat Shadow Kiuchi and steal his treasure, resulting in Kiuchi turning himself in to the police. As Kiuchi was brought in, Nagisa began to experience weird visions of the future, showing what would have happened had they failed to stop Kiuchi's crimes. Resolving to reclaim the desires of the masses, the trio works together as the Phantom Thieves, meeting new allies and fighting against more nefarious palace rulers. As the Phantom Thieves reclaim desires and change the target's hearts, Nagisa's visions became more frequent and extreme, implying that not everything is what it seems. ==Development==