Ys II: Ancient Ys Vanished - The Final Chapter is a direct sequel to Ys I: Ancient Ys Vanished - Omen. The game continues to use the action role-playing combat style of the first installment, which requires the player to have the protagonist run into the enemy to deal damage, without needing to press an attack button. The player should carefully choose the angles and the degree of contact with the enemy; otherwise, the hero will be killed. The player character can (and should) level up, perform quests for village people, gather money, and upgrade weapons and inventory, like in most other RPGs. The sequel offers a longer quest than the first installment and adds a magic arsenal to Adol's abilities. Among the magic spells are a fire attack, a time-stopping spell, and a transformation ability that allows Adol to pass for a monster and converse with enemies. Magic spells deplete Adol's magic points bar.

A bright light shot up from Darm Tower at the end of the first Ys, and Adol Christin is awakened by a young girl who finds him lying on the ground. She introduces herself as Lilia and tells Adol he is in the land of Ys. Finally, he was able to establish a connection between his world and this mysterious land! But finding the gateway to Ys is not enough; Adol must stop an evil entity that his archenemy, Dark Fact, served. And his foes already know where he is.