The PC/Mac version of the game, which was created by a different developer than the console versions, features completely different levels and gameplay from the console cousins.

In the GameCube version, there is an exclusive feature involving GC–GBA connectivity that allows a secret room to be opened in the GC version when connected with the GBA version of the game. While the PlayStation 2 version allows the player to land anywhere they want, in the Xbox and GameCube version the landing zones are limited. The GameCube, PlayStation 2 and Xbox versions of the game allow the player to access a broom and enter free-flight mode. There are also slight differences between the three other console versions of the game. Unlike other versions, most of the new spells learned from attending classes are upgrades from the previous game. It retains many elements and graphics from its predecessor but with some places in Hogwarts being expanded or moved as well as new mini-games that are played as the storyline progresses. The PlayStation version of the game is a sequel to the Harry Potter and the Philosopher's Stone game and was also developed by Argonaut Games. These challenges are all based on events from the book, for example, travelling into the Forbidden Forest and gathering ingredients for a potion Hermione is making. During the later parts of the game, the player will face challenges which are not time-limited and are not related to learning spells.

Each new spell is accompanied by a challenge, which the player must get through in a certain amount of time to complete that class period. Filling the gaps between these events are various classes, where the player will learn how to fly a broomstick and learn new spells for combating bosses, among other things. Throughout the course of the game, the player will encounter events that tie into the storyline of the second book.

Taking control of Harry, the player explores Hogwarts castle and grounds. The game's core gameplay is straightforward. It is based on the 2002 film of the same name. Harry Potter and the Chamber of Secrets is an action-adventure video game.

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