Crisis Core is an action role-playing game in which the player controls Zack Fair. The player moves Zack through and between open areas, allowing him to talk with non-player characters, interact with the environment, and engage monsters in battle. At save points, the player may opt to take one of the available side missions, and if so, Zack is moved to a special area to complete the mission, which usually involves defeating one or more monsters. If the mission is successfully completed, the player is rewarded with beneficial items, and often new missions become available. Whether the player is successful in the side mission or not, upon completion, Zack is returned to the save point in the main game.
Crisis Core uses a real-time combat system in which the player can move Zack around, initiate attacks, special abilities and spells, use items, and block or dodge attacks. Zack's abilities in battle are set by what materia he currently has equipped. Up to six materia can be equipped at any one time, which can impart special attacks, magic spells, or passive bonuses such as health increases or the ability to display the statistics of the current foe in combat. Materia are gained throughout the game through exploration, as rewards from side missions, as spoils of battle, or from shops. Materia can be fused together to make more powerful versions with improved bonuses; for example, fusing an attack materia with an elemental magic materia can create a new attack skill materia that inflicts elemental magic damage in addition to physical damage. Special items collected in the game can also be used in materia fusion to further increase the materia's power.
Crisis Core uses a slot machine-like mechanic to affect the combat system. The "Digital Mind Wave" (DMW) features two sets of three spinning wheels; one set with the numbers one through seven, and another with pictures of characters that Zack befriends during the game. The DMW automatically spins as long as Zack has at least 10 "Soldier Points", which are awarded to the player by defeating foes. If the DMW stops with the same three pictures lined up, Zack will then perform an appropriate Limit Break attack that can greatly harm an enemy or significantly heal Zack. Additionally, in this case, if the number slots give two or more of the same number, the materia in that slot will power up. Should the numbers line up as "777", Zack will gain an experience level, increasing his health, soldier points, and ability points. If there is no match in the pictures, matching numbers on the slots will grant temporary bonuses, such as limited invincibility or zero-cost use of skills and abilities. The chance of matching pictures is tied to the current Limit level, which is raised by taking damage in battle and reduced upon successful battles, and after certain storyline events. After collecting certain items in the game, the pictures on the DMW may also randomly change to summonable creatures, which have more destructive and beneficial Limit Breaks should the pictures match up.
Following completion of the game, the player will obtain a New Game Plus option. The North American and European releases of Crisis Core also have an added difficulty mode, which increases the power and health of enemies.