In every story, there is a Wildcard. There is a Velvet Room. There is a threat. There is a sacrifice. There is a hero.
In the year 2009 a young man named Yuki Makoto moved to Iwatodai where he attended Gekkoukan High School. There he met Yukari Takbe and Junpei Iori. One night he is awaken by Yukari and told about the Dark Hour, a hidden hour between one day and the next where people enter a sleep to protect them from the Shadows. Yuki summons his persona to save Yukari from a powerful Shadow and is recruited into the S.E.E.S where he meets Mitsuru Kirijo and Akihiko Sanada. Junpei soon joined the group and they got to work on climbing Tartarus. As time moved on Yuki met others like him such as Fuuka Yamagishi, Aigis, Ken Amada, Shinjiro Aragaki, and Koromaru. They battle against the strong shadows on full moons and scale Tartarus every night.
Mitsuru reveals the origin of the Dark Hour as her grandfather trying to contain Shadows. The project went sideways and the shadows formed the 12 strong shadows. Shuji Ikutsuki, the leader of S.E.E.S tells them that once they defeat the 12 shadows that Tartarus and The Dark Hour will dissappear.
After defeating the final shadow, however, they learn that they have been lied to and have released Nyx who created the shadows. Nyx is drawn towards Death who is disguised as Ryoji Mochizuki who Yuki had gotten close to.
It is revealed that ten year pior, the death shadow was created and Aigis sealed him away in Yuki when he was just a child. Ryoji warns that Nyx cannot be defeated and gave the users a choice. They can kill him and restart the year with no memory of the Dark Hour or Tartarus or fight Nyx.
After a month of thinking Yuki decides to let him live and fight Nyx. On January 31 the team heads up to fight Ryoji, now the avatar of Nyx. They defeat him but soon Nyx appears and the team is unable to defeat her.
Yuki is summoned to the Velvet Room and is given the power of the Universe and which allows him to seal away Nyx. The team lose their memories of the past year and Yuki sits on the roof of the school with Aigis as he slowly dies.
The team suddenly get their memories back and race to see Yuki just as becomes the seal and passes.
Two years later a boy moves to a new town called Inaba. This boy is YuNarukami. He lives with his uncle and cousin, Ryotaro and Nanako, and visits the Velvet Room. A mysterious murder rocks the quiet town soon after he arrives. He attends Inaba High and meets fellow student Yosuke Hanamura. When another victim is found after seeing her on the Midnight Channel, a odd occurrence that takes place on midnight of a rainy night, they go to investigate which leads to them falling into the TV World with Chie Satonaka.
There they meet Teddie and discover their Personas which they use to fight against the shadows and save others before they can be killed. They meet other persona users such as Yukiko Amagi, Kanji Tatsumi, Rise Kujikawa, and Naoto Shirogane. Together they save others and try to solve the turth behind the murders.
As things heat up Yu is arrested by his uncle when he suspects that Yu has some part in the murders. During his interrogation, Nanako was kidnapped and Dojima ends up getting hurt giving chase. When they find Nanako and free her from Taro Namatame, they learn that she is near death. She dies and the team confronted Namatame before Yu decides that he is not the killer. He spares him and reveals that Tohru Adachi, Dojima's parnter, is the murderer and Nanko recovered.
The team confronted Adachi who became possessed by Ameno-sagiri who is the cause of the mysterious and deadly fog. The team manage to defeat him and save the town but Yu instead questions the midnight channel and how he got his persona. Marie, a Velvet Room attendant, helps him discover that the gas station attendant was the cause of the channel who turns out to be Izanami.
Izanami was trying to turn the real world into that of the TV world and is actually part of Marie. The team confronted her but are unable to beat her until Yu gets the power of the World. He, with the help of Maire, summons his Ultimate Persona and defeats the god.
The TV world returns to normal just as the real world but is left blind from the power. Marie goes back to the Velvet Room and Yu returns home after promising to return.
Years later a new story begins as Akira Kurusu is punished for saving a woman from a man. He is sent to Tokyo where he lives with Sojiro Sakura and meets Ryuji Sakamoto. They end up stumbling into the Metaverse and are confronted by a shadow version of a teacher who is suspected of abusing his students. Akira awakens to his persona and the two escape with the help of Morgana. They decide to stop the teacher and they are joined by Ann who has a persona of their own. After forming the Phantom Thieves, the team decide to change the hearts of others.
Along the way they met several other users such as Yusuke Kitagawa, Makoto Nijima, Futaba Sakura, Haru Okumura, and Akechi Goro. As they change the hearts of others they discover something much bigger is going on behind the scenes and set out to stop it while Makoto's older sister, Sae Nijima, is investigating them. After they are framed for the murder of Haru's father the group allows Akechi to join so they can change Sae's heart.
Akira sacrifices himself to save his team but is caught by the police where Sae interrogates him. He tells her of the Metaverse and everything that has happened and Akechi comes in after Saw leaves to kill Akira revealing that he is the son of the man who framed Akira leading to him being sent to Tokyo. They change the heart of the man but Akechi passed away when he saved them.
Christmas Eve comes and the group realized that the world still sees them as criminals leading to them stealing everyone's heart from Mermentos. They end up being confronted by Yabathoth who has taken over the Velvet Room and replaced Igor. Morgana reveals that he was created by Igor to surve as his guide. Everyone dies but is brought back and face off against Yabathoth where Akira summons his Ultimate Persona. They defeat him but Akira becomes paralyzed from the waist down.
He proves his innocence and returns home. There he comes face to face with Aigis and Yu who tell him that Akechi is alive and that they need Akira's help. Akira agrees and now a new adventure begins.