Twin Goddesses are the pair of young Eldeens, Reah and Feena, who are revered as the Goddesses of Ys. They brought the Eldeen artifact Black Pearl with them to Esteria, and established the Kingdom of Ys. The Six Priests of Ys found that Cleria can be used to enhance magic originated from the Black Pearl while they were researching a way to recreate Emelas.
Although the Twin Goddesses are revered by most of the Ysicans, they enjoy having people treat them as friends. They grew close with a girl who snuck into their sky garden in the Solomon Shrine. They also have a great relationship with one of the Holy Knights that guarded them.
Later they realize that their imperfect control of Black Crystal has let demonic essence generate from the pearl, causing demons to appear in Ys. At the same time, one of the Six Priests, Cain Fact, has come out with his own ambition. He contacted some Darklings and planned an invasion to the Kingdom of Ys with an army of demons. The Twin Goddesses are forced to raise the land of Ys to the sky.
At this time, the captain of the Holy Knights, Saul Tovah and his second-in-command, Toal Fact volunteered to stay at the surface to buy some time for Ys to be raised to the sky. After the land of Ys was secured in the sky, the demons built the Darm Tower in order to bring it back down. The Goddesses then quietly escaped to the surface to find the culprit of the attack, as they have suspected one of the Six Priests has betrayed Ys.
After Cain Fact found out that the Twin Goddesses had run away from the Solomon Shrine, he quickly gathered a search team consisting of four Holy Knights (Galleon, Cecilia, Ramona and Roy), four sorcerers (Cadena, Miuscha, Rico Gemma and Hugo Fact) and three priests (Shion, Eolia, and Dino). He secretly ordered his son Hugo to kill his brother Toal. Before the search team departed for the surface, Yunica Tovah, an apprentice knight, asked to join the search team because she vowed to protect the Goddesses.
And thus started the story of Ys Origin.