The Alaya Shrine in Persona 2: Innocent Sin.
The Alaya Shrine, also known as the Araya Shrine depending on the game and the translation played due to R and L being interchangeable in Japanese, is a location in both Megami Ibunroku Persona and Persona 2, noted for its ties with Philemon.
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Megami Ibunroku Persona[]
The Alaya Shrine appears in Mikage-cho. It is here where the party reunites with Setsuko Sonomura after escaping from the Hospital and has a second encounter with Philemon.
Later in the game, after the death of Takahisa Kandori, the party returns to the shrine to contact Philemon, who tells them that Maki Sonomura's soul is calling out to her Ideal Self and the protagonist from within the Sea of Souls. He reveals that the Alaya Shrine is connected to the Sea via way of the Alaya Cavern and sends the two to contact Maki.
Persona 2: Innocent Sin[]
Maya with Tatsuya, Lisa, Jun and Eikichi.
A second Alaya Shrine also appears in Sumaru City at the foot of Mt. Iwato. Prior to the events of the game, the five protagonists would play at the shrine as children, forming the first incarnation of the Masked Circle. After Maya Amano, the eldest of the group, revealed that she had to move away the following day, the others panicked and locked her in the shine, believing that they could make her "miss" her moving by doing so.
That same day an insane arsonist known as Tatsuya Sudou would be driven to set fire to the shrine. Maya awoke to her Persona and broke out of the shrine, only to be confronted as a witch by Sudou. Maya would be saved by Tatsuya Suou awakening to his own Persona and burning out Sudou's eye. Nyarlathotep took full advantage of the mishap to target and use everyone involved as pawns for his game with Philemon, presenting them with half-truths and misinformation of the situation to turn them against each other, turn Jun Kurosu into a madman and eventually cause the destruction of the world through using them to spread world-destroying Rumors.
After the incident, rumors spread that Maya had died in the fire and her ghost still haunted it, causing a rumor ghost modeled after her to lurk around the shrine and Mt. Iwato.
Persona 2: Eternal Punishment[]
Eikichi feeling a wave of sadness.
After Maya's final battle against Nyarlathotep, Eikichi Mishina, Lisa Silverman, and Jun Kashihara meet by chance at the shrine for the first time in this timeline. Eikichi is the first at the shrine. Jun arrives and Eikichi replies he felt like he left behind a very important memory here. After Jun agrees, Lisa arrives and says she feels very sad. Jun says he feels a great void in his heart.
In the PSP additional scenario, it is revealed that an equivalent event to the shrine fire was orchestrated in this timeline by Nyarlathotep as well, with Sudou instead killing and dismembering Shiori Miyashiro's brother Takuya there.