During a wave more troops can be placed or an Esper can be summoned for the prices of five crystals. For each enemy defeated the player is awarded money which can be used to buy new troops, power crystals or to level up their current troops, making them stronger.

When they have laid out their troops in a fashion they like they can then start the wave of enemies. The player's first objective is to deploy units. If the player should lose all twenty of their crystals then it is game over. If an enemy gets from one end of the path to the other, the player will lose one crystal. There are a total of thirty waves, each one consisting of a specific type (or types) of enemy and the enemies get stronger with each progressive wave. The object of the game is to defend a path which waves of enemies will walk through. The Wii versions of the game are numbered differently, only R1 and R2. Finally the complex maps in W3 are intended to challenge even the most seasoned players. In W2, the introduction of Power Crystals opens up new doors, allowing for deeper, more detailed strategies. In W1, players can learn the game basics. There are 12 stages total in three different game versions, W1, W2, and W3. While the iOS, Android, Wii and Fire OS versions have been removed, offline versions for PlayStation 3, PlayStation Portable, and Xbox 360 remain available.

The game officially reached end-of-life as of May 31, 2016. A remake of the game that goes by the name of Crystal Defenders +Plus was released for iOS featuring similar game content, smoother gameplay and additional downloadable maps. IOS, Android, Xbox Games Store, PlayStation Network, WiiWare Crystal Defenders, originally released in Japan as Crystal Guardians, was a defensive strategy game in which players deploy Jobs from Final Fantasy Tactics A2: Grimoire of the Rift, such as Black Mages and Soldiers, to fend off encroaching enemy hordes and prevent them from stealing their party's crystals.

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