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.
Megami Ibunroku Persona
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
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 arsonist 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.
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
After Eikichi Mishina, Lisa Silverman, and Jun Kashihara are rescued from Nyarlathotep by Maya and her party at the end of the game, they 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.