Spells are learned progressively via lesson levels, and unlock increasingly complex puzzles. The story follows a linear progression, separated into levels with a specific end goal. In the PC versions, the game is played like a third-person action and puzzle game. The player controls the character Harry Potter from a third-person perspective.

1.5 GameCube, PlayStation 2, and Xbox version.

Critics commented on the game's accessible gameplay and its unimpressive graphics (2003 versions) while others said the game's license would be the only thing to draw in fans. The story follows protagonist Harry Potter, who, after discovering he is a wizard, is sent to Hogwarts School of Witchcraft and Wizardry where he makes friends and receives magical training, and along with his friends stop Lord Voldemort from returning to power. The versions on different platforms differ greatly from each other and do not follow the same level structures or gameplay. A different game bearing the same name was made two years later for the GameCube, PlayStation 2 and Xbox in December 2003. Philosopher's Stone was initially developed for the Game Boy Advance, Game Boy Color, Microsoft Windows and PlayStation in November 2001. It is based on the 2001 film of the same name. Harry Potter and the Philosopher's Stone (released in the United States as Harry Potter and the Sorcerer's Stone) is an action-adventure video game.

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