The events of Ys Origin take place 700 years before those depicted in Ys: The Vanished Omens; it is the first game in the timeline of Ys, and a prequel to the entire series. It is also the first Ys game in which the main protagonist is not Adol Christin, the red-haired swordsman and recurrent hero of the series.
There are three main playable characters in the game: Yunica Tovah, a young apprentice knight; Hugo Fact, a skillful magician; and a mysterious person known as The Claw. These characters venture to the sinister Darm Tower, each having his/her own motives. The three also vary in gameplay style: Yunica plays similarly to Adol from the previous games, specializing in melee combat with swords and axes; Hugo fires magical bullets with his staff and has access to other types of magic; The Claw is distinguished by his speed in close combat.
The fast-paced action RPG gameplay is similar to the one adopted in Ys VI: The Ark of Napishtim and Ys: The Oath in Felghana. As the story progresses, characters acquire skills that can be combined in order to extend battle strategy. Some of the bosses from the first and the second Ys re-appear in this game.