Eleven years have passed since Arle Nadja, magician girl extraordinaire, has defeated the evil as part of her examination in the magical school. Now she is sixteen and she can still remember the spells she has learned long time ago. One day she meets a fresh young man who without any apparent reason casts a powerful spell on her. Arle finds herself locked in a prison cell. Grabbing the key, she runs out of the cell, only to find out she is imprisoned in a huge dungeon populated by vicious monsters...

Madō Monogatari II retains the gameplay system of the previous game. You navigate Arle through first-person 3D dungeons. Enemy encounters are random. During the turn-based battles, you can attack only with various types of magic. Since you don't see your own hit points, the key to winning the battles is to choose appropriate spells against various types of monsters.