Beat the game and make a cleared game save file. Reload any save before you beat the last boss and go to the world map. You will see a new area called Old School Building which leads to the bonus dungeon.
Inside you'll find the standard array of post-game completion challenges, including new very powerful monsters with different elemental nullifications including physical type attacks, a stronger version of the Final Boss and a boss Cameo from Atelier Iris 3
After beating the game once you'll unlock the extras menu in the title screen. With each subsequent playthrough more will be added to the Endings and Encyclopedia sections.
The Menu contains:
Gallery - Picture Gallery of all the characters and ending portraits based on your saved game.
Database - The Encyclopedia of Monsters, Alchemy Items, and Recipe
Music - The OST in game
Cast - Listen to the thanks of the Japanese voice cast
Endings - View all unlocked endings
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