Irene is a student at the Tirisfal Fortress, the magic academy where her sister Annie is one of the tutors. After a precious treatise containing a demon-summoning spell is stolen from the archives, Annie is accused of the theft and threatened to be banished and imprisoned. Irene starts to search desperately for the missing book to clear her sister's name, scouring all the rooms and interviewing all the staff.
Like its predecessor, Magic Academy 2 is a hidden object game utilizing the familiar NevoSoft interface, sharing its main design with other titles developed by the company. Most of the time, the objective is to find a series of assorted items on a screen depicting a location around the academy. The list of required objects appears at the top of the screen, showing the names or silhouettes for each entry. Some scenery objects like doors, chairs, tables and curtains can be moved to reveal a concealed item. The hint button makes one of the required objects sparkle, but takes some time to recharge after use.
Some items are stored in the inventory area at the top, to be used later when solving puzzles. The inventory objects have to be dragged and dropped on appropriate and logical portions of the scenery. For example, a key can be used to unlock a door. Some puzzles take place on a separate screen, where the player has to complete a mini-game, like solving anagrams, finding all the differences between two similar images, restoring broken electronic circuits, repeating patterns on a pentagram, clicking on matching runes, assembling jigsaw puzzles and other challenges.