The game is set six months after the events of Persona 5, The protagonist and Morgana return to Tokyo for a reunion with the other Phantom Thieves of Hearts to spend their summer vacation together on a camping trip. To determine the camping preparations, they use a popular application called EMMA. While going to Shibuya to buy the necessary tools, they pass by a rising idol, Alice Hiiragi, who gave the protagonist a card requesting them to input "Wonderland" into the EMMA app for her special event. Upon entering the keyword, however, he, Morgana and Ryuji are transported into a mysterious alternative version of Tokyo called a Jail, where they encounter the ruler called King who is Alice's Shadow self, and a sentient A.I. named Sophia who is able to fight Shadows who joins their party. They learn that EMMA, similar to the Metaverse Navigator, enables them to enter Jails. Hearing rumors that people have been attacked by Shadows in Jails that leaves them behaving strangely in the real world, Joker and his friends once again establish the Phantom Thieves of Hearts.
