Persona 4 opens with the Protagonist arriving in Inaba to live with the Dojimas for one year, as his parents are working overseas. Within days of his arrival, a journalist is found dead, her body tied to a lamp post; Saki Konishi, who made the discovery, is later found dead under similar circumstances. After the protagonist and his friends travel to the TV world, they discover Teddie, who helps them travel freely between worlds. They awaken to their Persona abilities, and, realizing that the murders stem from Shadow attacks in the TV world, are able to rescue several people. Chie, Yukiko Amagi, Kanji Tatsumi, Rise Kujikawa and Teddie accept their Shadow selves and join the group as Persona-users. Mitsuo Kubo, another high school student who goes missing following the death of a Yasogami teacher, claims credit for the murders when he is rescued; it is eventually learned that he only killed the teacher and played no part in the other murders. Naoto Shirogane, a nationally-renowned teenage detective investigating the case, is also rescued and joins the party, who learn that "he" is actually a female who assumed a male identity to gain recognition.
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vents come to a head when the Protagonist is mistakenly accused by Ryotaro Dojima of having a role in the murders. Nanako Dojima is kidnapped while the Protagonist is being interrogated. Ryotaro engages in a high-speed pursuit with the culprit, resulting in them crashing into each other; the culprit escapes with Nanako through a television set in his truck, and Ryotaro entrusts her rescue to the party. The group tracks them down within the TV world; the culprit, Taro Namatame, attacks them, but is defeated and both he and Nanako are taken to the Inaba hospital. When Nanako appears to die, the group confronts Namatame; the player as the Protagonist must help the others realise that Namatame is not the killer by pointing out the lack of a proper motive, and subsequently work to determine that Ryotaro's assistant, Tohru Adachi, is the true killer. Failure to do so ends the game with the party being unable to solve the case and the recurring fog permanently setting in, the latter of which will eventually result in humanity's demise.
Having identified the culprit as Adachi, the party locates 
him within the TV world. Adachi explains his motives and ideals to the group; his claims are dismissed by the party. After fighting Adachi, he is possessed by Ameno-Sagiri, the God of Fog, who reveals that the fog is lethal to people and will eventually wipe out humanity. Upon his defeat, he agrees to lift the fog, congratulating the party on their resolve. Defeated, Adachi agrees to assume responsibility for his actions and turns himself in.
The game moves forward to the day before the Protagonist is to return home; if the player assumes the story is concluded, then the game ends with the party farewelling the Protagonist as he departs Inaba. In fact there is still one unresolved plot element, the origin of the Midnight Channel, and if the player realizes this and enters the party's meeting place while ignoring the game's attempts to steer them away, the Protagonist meets with the party and together they resolve to put an end to the case.
The Protagonist encounters the petrol station attendant, who reveals himself to be Izanami, a goddess and the mastermind behind the game's events, who plans to eliminate humans by merging the TV world with the human world, which is the cause of the recurring fog. The party tracks Izanami down within the TV world and battle her, but is at first unable to win; a defeated Protagonist is given strength by the bonds he has forged with those around him, and with this power awakens a new Persona, which he uses to defeat Izanami. With the source of the fog defeated, the TV world, actually the world formed from people's thoughts and desires, is restored to its original form. The game then ends with the party farewelling the Protagonist the following day, and a post-credits scene depicts the group resolving to remain friends forever as the Protagonist examines a photo of the party.
