Ys I begins with a cutscene showing the main character, Adol Christin, gazing out to sea at the Stormwall which appeared around the island Esteria six months ago. Determined to investigate the situation, Adol sets off towards Esteria on a small boat; however, it is sunk by the storm and Adol washes up on the shore of Esteria. He is saved by a villager named Slaff from the port town of Barbado. Adol recuperates in the home of Barbado's doctor and learns that Slaff is both the doctor's son and the head of the town's militia. The militia was formed when demons and monsters appeared on the island, at the same time as when the Stormwall formed. The Stormwall cut Esteria off from the rest of the world and completely halted the trade of silver, which is mined on the island.
Adol sets out to find out more about the island's situation in the largest town of Minea. There, he encounters a female troubadour named Reah. Reah is searching for her Silver Harmonica, which had been stolen, part of a rash of silver thefts that have occurred in the town. Linked with the thefts are sightings of a man in a dark cape. Adol then encounters the fortune-teller Sara, who tells him that she had a vision that a fiery-headed swordsman who would play a key role in Esteria's fate. She tells Adol of the six Books of Ys, named after the ancient kingdom that existed on the island seven hundred years ago. The Books of Ys contain the complete history of the rise and fall of Ys and will be instrumental in saving Esteria. Sara informs Adol that one book is in the Shrine of Solomon and sends him to the town of Zepik to speak with her aunt Jeba to learn more.
In Zepik, Jeba gives Adol the Key to the Shrine. Adol also meets the mayor of Zepik, and learns that the town's treasured Silver Bells have been stolen. The Silver Bells gave off a sound that drove evil away, and without it, Zepik is vulnerable to demon attack. Adol assumes a mission from the mayor to negotiate the return of the bells from a bandit group in the area. When Adol meets with the bandit leader Goban however, Goban protests that his group only steals from the corrupt to give to the poor, and that in fact all of the bandits' silver possessions have been stolen from them. Adol leaves them and enters the Shrine of Solomon.
Ys II
The story of Ys II continues off immediately from the end of Ys I. The game begins with an animated cutscene showing a figures in a dark room talking to a glowing orb about Adol. They are impressed by his having conquered the Tower of Darm, and decide to continue to observe him. The view then shifts to the final moments of Ys I, with light emanating from the Books of Ys and surrounding Adol. Adol then suddenly is flown high into the sky by the magic from the books, as Feena and Reah watch from a cliff outside the tower. The magic energy deposits Adol and the Books of Ys in a flash of light in a field, where he is discovered by a girl. The view pulls back to show that Adol has landed on an island floating in the air.
A flashback to 700 years ago is shown: the two Goddesses of Ys are standing around a large glowing orb with their eyes closed, deep in concentration. Outside, a horde of demons lays siege to their location. A flying island is created, and soars high up into the sky, leaving a great crater behind. In the modern day, this island floats far above the Tower of Darm.
When Adol wakes up, he weakly asks the girl where he is. She tells him that her name is Lilia and that he is in Ys. Adol is brought to Lance Village and recuperates in Lilia’s home. When he wakes up, Lilia’s mother tells him about Ys and the surrounding area. Lilia’s mother also asks Adol to deliver a letter to the town doctor, Dr. Flair, discussing Lilia’s illness. Speaking to villagers of Lance, he learns that demons appeared on the island six months ago, which forced the villagers to abandon the nearby Rasteenie mines. In addition, most of the villagers are aware that there is a world outside of Ys.
Adol goes to the town clinic to look for the doctor, but the doctor is not present. Suddenly, a flying pigeon arrives at the clinic bearing a message from the doctor, which states that he has been trapped in the Rasteenie mines by a cave in as he was picking herbs. Adol is asked to rescue the doctor from the mines, as only Adol could fight the demons inside. Adol agrees, and meets with the elder of the village to gain permission to enter the mines. The elder consents, but also mentions that he briefly saw two girls that resembled the Goddesses while walking in the ruins surrounding the mines. The elder also tells Adol that his having possession of the Books of Ys shows that he was guided by the spirits of the Priests of Ys to the island. The elder reveals to Adol that there is a place called the Sanctuary of Toal, connected to the Rasteenie mines, which houses statues of all six Priests, and that Adol should return the proper book to each statue in order to learn his purpose on the island.
