Here’s the awfully long concept story of Persona 6,
The story starts with the Protagonist waking up on the train after having a flashback of being falsely arrested and sentenced to yearly probation then having have been transferred to Okinawa where she has to stay with her police officer aunt Aoi Kasagano and little cousin Kairi. Soon after getting accepted into Westbrook Academy and her luggage into the house, the Protagonist awakens in the Velvet Room (which takes the form of a train) where Igor tells her that a powerful threat will soon come and she must raise a team in order to overcome this “threat”. After the first day of school, the Protagonist meets Anna Walker and Ryu Taiyō who discuss a strange incident called “Psychotic Breakdowns”. The following night, the protagonist discovers an app which opens a portal which she pulls herself out of. The next morning, the Protagonist shows Anna and Ryu the app that send them to Dimension X (Cross) where they find the palace of their abusive gym teacher Hidoi Kyōshi which takes the form of a military base. The trio meet amnesiac husky Bucky and the Protagonist awakens her persona Elena.
When the protagonist and Ryu visit a second time, they and Bucky meet Aigis who seems to have no memory of the past three months. Later, Anna and Ryu awaken their personas and the heroes discover they can steal the emotional root of the palace aka “Treasure” to change the heart of Kyōshi which they succeed in. After a celebration, the group decide to continue with changing the hearts of the corrupt society they live in and bring back Aigis’s old team name S.E.E.S (Specialized Extracurricular Execution Squad). Soon they start going on a massive change-of-heart spree which are of a embezzling director; a villainous mob boss; a evil priest who brands people for the slightest of mistakes; and Megumi and Aika’s mother Tao Otani. As the numbers of members and popularity start to grow, so does the concerns of the Tao and detective sisters Asuka and Namaari who later join S.E.E.S during the Otani Arc.
After changing the heart of Tao, Aoi discovers the protagonist is a member of S.E.E.S via a calling card on the coffee table. Aoi then takes the protagonist to the police station for interrogation where Tao asks her questions about Dimension X, as Tao leaves the room, Asuka breaks in with a guard with the guise of rescuing the protagonist but Asuka betrays her by setting the interrogation room on fire and telling her that the police chief Fuhai Kurai is the man behind the protagonist’s probation. The protagonist is assumed dead but was rescued by Tao due to her having suspicions of Asuka carrying gasoline with her.
S.E.E.S discover that Chief Kurai is planning to become president of Japan and later the World and decide to change his heart one last time. While they infiltrate the palace, S.E.E.S meet with Asuka who reveals herself to be behind the psychotic breakdowns and she says she did it to entertain herself and due to Namaari upstaging her in the Detective world. After being defeated the first time, in a desperate fit of rage, Asuka goes psychotic and summons the somehow resurrected Magatsu Izanagi and becomes the rumored Black Knight figure that multiple shadows mentioned earlier in the game.
Asuka is finally defeated and despite being encouraged by S.E.E.S to follow her true feelings, she refuses to continue being upstaged by Namaari and attempts to commit suicide by shooting herself in the head before a cognitive copy of her appears and the real Asuka sacrifices herself to save S.E.E.S. Then they make it to the treasure route and release a worldwide calling card which infuriates Kurai. S.E.E.S encounter Shadow Kurai which they fight and defeat. The change of heart is a success and S.E.E.S celebrate until Namaari betrays them and steals a coin that Asuka gave the protagonist before possibly dying.
The team follow Namaari into Dimension X where she reveals that she is also involved with Asuka as they are both the imposters and she is possessed by the threat aka the Malevolent Force as she calls it. The Malevolent Force takes over Namaari and reveals that Namaari took the form of the protagonist temporarily and started her probation on purpose due to the Force and Igor seeing potential in the protagonist and reveals that he resurrected Magatsu Izanagi and wiped Aigis’s memory. Namaari then falls off the palace roof seemingly killed herself until the Malevolent Force reveals its true form, Lucifer.
S.E.E.S then attempt to fight Lucifer but to no avail until he banishes them back into the real world but Dimension X starts to merge with the Real World via Lucifer’s magic and piles of Shadows swallow S.E.E.S except for the Protagonist. Without the bonds of her friends, the Protagonist slowly starts to fade away due to the despair of loneliness until Margaret (The Velvet Room Attendant) slaps the Protagonist out of her trance and tells her that “no matter if the Protagonist wins or loses, she will never be alone no matter what” and gives her a crystal called “The crystal of truth”. Encouraged, the Protagonist fights Lucifer again but she places the crystal inside her wand, turning her into “the White Mage”, her wand becoming Excalibur, and the Protagonist awakening her Ultimate Persona, Morgan Le Fay.
The protagonist defeats Lucifer with Morgan Le Fay’s power and Excalibur’s “Myriad Truths Ver. 5”, Lucifer accepts his defeat and vows to never harm anyone again as he returns to slumber. S.E.E.S then are each granted a wish and are returned to the Real World as Dimension X and Bucky fade away. The team then promise to keep seeing each other and remain friends no matter what. The next few months pass by (And Bucky is revealed to be alive due to Igor granting him a second chance in life.) and the Protagonist is supposed to go home by decision and two different endings happen but either one ends with S.E.E.S still bonding.
If you choose to leave, S.E.E.S share a heartfelt and tearful goodbye as the protagonist boards the train home.
If you choose to stay, S.E.E.S share a group hug and the Protagonist starts a new life in Okinawa and S.E.E.S meets her parents while “Ocean Man” by Ween plays in the credits