Persona: Trinity Soul

Ryō Kanzato, an officer in the Ayanagi Police with the rank of Superintendent, had been dispatched to a Japanese Coast Guard PLH ship after Japanese Coast Guard crewmembers discovered that their Deep Submergence Vehicle had its entire crew missing, baffling some of them. Meanwhile, mysterious deaths had been reported throughout the city once more. Ryō had rescued Yumi Tasaka, who had been under police custody, from being killed by an unknown assailant with his Persona. Ryō's siblings, Shin and Jun, arrive back in Ayanagi City in the course of his investigation and battle against the assailant with his own Persona. After Shin's arrival, his Persona had awakened and killed the same assailant's Persona after it had threatened him earlier during a walk around the city.

Unsure about whether or not the events from the previous night were a dream or not, Shin goes to his new high school. After falling asleep, he is awoken by Megumi Kayano. After going to explore, he meets Takuro Sakakiba and performs a shadow extraction. While performing it, a Persona comes out of Takuro. Will Shin's come out too?

Hearing a loud noise from their karaoke room, Shin and Takuro go to investigate and find Kanaru covered in blood shielding Megumi. After looking around the room, the two notice one of the bodies is turned inside out. Later at the police station, Ryo questions Shin about why he was there.

Thinking about what Inspector Itou said to him the previous night, Shin decides to take a look at Ryo's files and look for the list. Before he can, a loud noise attracts his attention and he finds Jun in an old storage shed looking through things. Later that night, Jun wants to eat dinner with Ryo. After an argument with Ryo, Shin accidentally knocks the dinner out of Jun's hands, causing to Ryo leave. After getting on Ryo's computer, Shin finds the list Inspector Itou told him about.

Shin hears Takuro, Megumi, and Kanaru talking about a student who dissappeared. Upon hearing the students name, Shin realizes he is one of people on Ryo's list. Later that night, Shin hears Jun leave and goes after him. Upon catching up he learns that Jun is hearing a voice in pain. Deciding to go with his brother to find it, Shin and Jun end up at an old abandon building.

When the actor that is supposed to act as police cheif for a day does show up, Megumi and Kanaru are chosen to replace them. Meanwhile Ryou comes across a man in a bear costume who seems to be in some trouble. When Ryou leaves the man for a second, he returns to find an empty bear costume. Now Ryou must take his place.

Shin, Jun, Megumi, Kanaru and Takurō alongside Yumi go to an inn in the outskirts of Ayanagi City for a break. During this time, Takurō tries to train himself to use his Persona. Megumi had reawakened her Persona after seeing Yumi grab a white feather from the top of the lighthouse, who almost died if Megumi's Persona didn't help her in saving Yumi. Meanwhile, Shin meets up with the mysterious woman after his Persona had attacked her in the beach.

A long time friend of Morimoto transfers into the school, and along with her, mysterious and bizarre "pranks" start happening almost every night in the grounds. The group decides to investigate these incidents by going to the school at night. They divide into two teams: Shin, Jun and Kanaru, and Takurō and Megumi on the other. With the two older boys overly scared, the girls lead on to find Morimoto's friend collapsed on the floor of the science room. Meanwhile, Jun senses a troubled persona nearby and disappears to the camphor tree on the school's yard, and uses his own to comfort it.

Shin goes along with Eiko to examine the submarine whose entire crew just disappeared. Eiko soon reveals the decision Ryou had to make in order to save Jun. How will this affect how Shin sees his brother?