In episode 1 of Ayaka, the protagonist Yanagi Yukito receives a letter from Inou Sanji, a friend of his deceased father, inviting him to return to his birthplace, the Ayaka Islands. Yukito grew up in a foster family since he was five years old, after his father passed away. He first attends a school graduation ceremony and later prepares to leave the foster family.

Suddenly, an eccentric man named Sagawa Jingi appears, claiming to have been sent by Inou Sanji to escort Yukito to the Ayaka Islands. Jingi possesses strange abilities, such as pulling Yukito into a bag that acts like a portal. The two reach the islands aboard a train called the Marine Liner, which travels over the sea.

Upon arrival, Yukito is warmly welcomed by the islanders, including Inou Sanji, the mayor of Ayakashima City, and Amamiya Momoko, the landlady of Yukito's childhood home. They all move into Yukito's former house. Jingi reveals to Yukito that his father was a Ley Master, a person with mystical abilities. He also mentions that Yukito possesses latent powers inherited from his father. The locals know nothing about Yukito's mother, as his father never spoke of her.

Yukito confides in Jingi that he has distanced himself from others since childhood because his uncontrolled emotions once caused a river to attack another child. He believes his emotions are linked to a mysterious power he cannot control.

Jingi is ambushed by another spirit, and Yukito instinctively uses his power to save him. Jingi praises Yukito's strength but advises him to control his abilities. Jingi offers to train him, and Yukito agrees. They head back to the house together as Yukito reflects on the kindness and support of the islanders, developing a sense of belonging.

The episode sets the foundation for Yukito's new life on the Ayaka Islands, where he must learn to understand and control his powers with the help of Jingi and the community.