Set in Al-Revis Academy, an academy that teaches children alchemy. The academy has now fallen to the ground, but it still goes on. However, the school's budget is low and they have to find sponsors so they don't have to close the school. Marta, the spokesperson of the sponsors started a new class, the Art of Battles in an attempt to get more students to join, then Zeppel, the principal makes Flay the teacher of the class. Roze joins that class. Toni (yet another returning character) teaches Alchemy the class which the second main character, Ulrika attends.
There are two main characters for this game: Roze and Ulrika. The game gives you a choice of which character you want to play with at the beginning of the game. There are different storylines for each of them but the gameplay is the same, create items with alchemy, fight enemies using a turn-based system using individual and group techniques just like in Mana Khemia Alchemists of Al-Revis.
- Dual Battle - Mana Khemia 2 adopts a unique type of turn based battle system. You will have a set of attackers and supporters that switch in and out throughout the battle with attack/support actions.
- Massive Item Crafting - Over 100 items to craft. Players can search for ingredients throughout the world and create new items using what you’ve found.
- 2 Main Characters - There are 2 separate stories ready for Mana Khemia 2. Depending on how you played the game can alter the ending, so there are 2 storylines for the 2 main characters.