The game begins with a white wall as people arguing are heard on the other side. The wall eventually cracks and shattered, revealing a massive green abyss. Ghostly images of people float through the abyss and groan in pain, unable to remember where they are. The protagonist is then seen sitting on a floating rock in the abyss and attempts to keep their mind active by grasping on to their memories, including the most basic such as their own name. After remembering this, they attempt to recall what led them up to this moment, a blast of burning energy emitting from them as they do.
The game then rewinds time to back to the beginning of the year, where the protagonist is shown moving into a new house after their father gets a new job. While on the train to Tokyo, they find a teddybear on the ground and attempt to give it back to a little girl. The girl accepts but the mother pulls them away from the protagonist, who they appear hostile towards. The mother claims they've "heard what they did" before getting off the train at the next stop and walking as fast as possible away from the protagonist. The protagonist quickly makes their way to their new home in Tokyo suburbs only to discover their home's front lawn is incredibly overgrown and their father is nowhere to be found, leaving behind a note reading "mow the lawn". While upset, the protagonist does so and attempts to enter their house only to discover the door isn't even unlocked for them. Due to this, their neighbor, Mahiro Asai, allows them to stay in his house for the time being. Unfortunately, the protagonist's father doesn't return to them and they end up staying the night at Mahiro's.
The protagonist lives in Mahiro's attic and sets up their computer, browsing the internet to pass the time. While doing this, they discover a conspiracy website that reveals several people have been going missing across Tokyo for unknown reasons. They then hear a voice behind them and turn around, revealing the walls of their room have become green code of ones and zeroes. A texture slowly forms over the code, turning the room into a chamber filled with hard drives and wires with three people standing in the middle of it all. The three introduce themselves as Walter, Jenine, and Beatrice and stand aside, revealing their master sitting in the middle of the room. The man reveals his name is Igor and welcomes the protagonist to the Velvet Room.
After an introduction to the Velvet Room, Igor ends the protagonist's visit by telling them he's interested in seeing their full potential. Igor then tells the protagonist to wake up, which they do, revealing they fell asleep while searching the web. Assuming the Velvet Room was just an odd dream, they head downstairs where they're informed that their father left a message for them. They play the message, which is just their father telling them he'll usually be at work and can't come to visit the protagonist very often, telling them to live with the Asai's for the time being. While disheartened, the protagonist is comforted by Mahiro. Mahiro then gives the protagonist directions to their new school and they walk there. The protagonist is sat beside popular student Kaori Fujio, who they attempt to introduce themself to but are blown off. After their first class, the protagonist is introduced to Eiji Ishimura, who the teacher asks to show the protagonist around. They do so and, while showing them a garden-like part of the school, the pair run into a group of bullies, consisting of Goro Masuya, Kazumi Oshio, and their leader and Goro's brother, Daizo.
The Masuya gang picks on Eiji in front of the protagonist, who decides to help out and is beaten by Daizo for their troubles. Luckily, Eiji still appreciates their help and asks if the two can hang out later. The protagonist, while not sure about Eiji, agrees as to not seem rude. The protagonist visits Eiji's home, where they discover Eiji's parents are also usually out but in Eiji's case, they leave him home a lot due to needing him to take care of his baby sister. Finding out they have this in common, the protagonist warms up to Eiji a bit more and the two begin to bond over the course of the night. However, things take a sudden turn when they get a notification from a website called P.New.
The pair initially dismiss the notification due to thinking it could be a virus but after it appears over and over they decide it might be important and click on it. A green light then flashes from the computer screen and scans the protagonist, who slowly transforms into green lines and disappears. They then wake up inside of what appears to be a digital world and hear an odd mumbling voice in their head, which they had been hearing a few times throughout the week. However, the voice stops when Eiji suddenly appears beside them, with him claiming he also clicked the link in order to make sure the protagonist was okay. Eiji is taken aback by the sight around him but his wonder turns to terror when he spots a figure in the distance. The figure charges towards Eiji, revealing itself as another version of him with glowing eyes.
The separate Eiji begins attacking Eiji, screeching about how much it hates him. In response to seeing this, the voice in the protagonist's head flares up and begins talking to them, asking the protagonist to speak its name. The protagonist does, calling out their first Persona Ezekiel and battling the other Eiji. When it is defeated, Eiji confronts his other self and asks if it's him. In response to this, the other Eiji explodes into energy that is absorbed into Eiji, though Eiji doesn't feel any changes within him. After this, the pair look for a way out and are unknowingly followed by a short person. Eventually, they find a door in the middle of nowhere and decide to enter, though they are confronted by the short person before they do.
The short person, identified as Seth and mistakenly referred to as a clown by Eiji, informs them that they were about to enter a door to a "Databank" and that doing so without a guide would've been suicide. The three enter the Databank where they are almost instantly confronted by strange looking creatures which Seth refers to as "Shadows". Seth helps the protagonist battle the Shadows and they are eventually met by the Shadows' leader, who appears to be the girl that the protagonist met on their first day, though Eiji quickly realizes that they are more than likely a Shadow of them like how Eiji had a Shadow of himself. Eiji gets ready to face them but Seth claims that would be foolish with how weak the three are at the moment. Due to this, they decide to run and eventually find their way out of the other world. When out, Eiji informs the protagonist that his parents are coming home soon and they decide to leave, though they agree to explore that world the next day.
The protagonist returns home and falls asleep, once again meeting Igor who informs them that they are happy they finally unlocked their Persona and warns them of an upcoming tragedy that they have been chosen to face, though he doesn't believe the protagonist will be able to face it alone and requests them to befriend more people in order to save the world. While hearing this, a blue butterfly begins floating around the protagonist and eventually lands on their head, causing them to wake up at their computer again. The protagonist then gets up and heads to school where they talk to Eiji about their encounter with the ".New" world. During this conversation, the pair overhear Kaori Fujio talking about a "weird dream" she had where she was stuck inside of a computer world. Realizing what this means, the pair decides to talk to her after class.
They confront her at lunch and talk to her about her dream, revealing that both of them were also stuck in the .New world for a while. Realizing they needed Seth to get out, the pair asks Kaori how she escaped without any help. She claims that she "woke up" and continues to claim what happened to her was a dream, believing the two are making a very odd joke. She attempts to leave them behind but, wanting to prove to her that .New is real, Eiji invites Kaori over to his house and claims that he'll be able to access the .New world and prove that everything that happened in it was real. Kaori reluctantly agrees, realizing they won't leave until she does. Later that night, the protagonist, Eiji, and Kaori all meet up at Kaori's house where Eiji types in the P.New website only for it not to work. Now convinced this was a prank, Kaori attempts to leave only for the protagonist to reload the page and be sucked into the computer, shocking Kaori.