The game is a third-person shooter, with a first-person viewpoint that is also selectable. A cross hair is utilized as an aid to shoot enemies.

Battle can be initiated at any time during exploration. Vincent has an HP Bar, as well as mako points (MP), akin to that of magic points. Leveling up is possible, though the opportunity to do so is given either at the end of the chapter or dying mid-chapter. The result of either event yields points, the value of which are decided based on Vincent's performance and whether certain conditions are met. The points can then be converted into experience or into gil.

Vincent's main weapons are a set of three guns: a handgun, a machine gun and a rifle. All are upgradable during many points in the game. Ammo is obtained either through shops or in the field. The weapons can also be customized, using a variety of accessories that increase power or reduce weight. Materia is used to provide magic shots that consume MP.

The option using Limit Breaks is also available. Vincent's first limit break, the Galian Beast is available by using up MP (Japanese version) or a single-use item called "Limit Breaker" (US and PAL versions). Another limit breaker is Chaos, though it is not available up until the game's final chapter; it is automatically given to the player at that point.

Being modeled after many first-person and third-person shooters, the game takes a few liberties and implements minor features that are featured in many games that are similar in genre. A blinking disc icon appears whenever the game loads data from the disc, something akin to many shooter games. The game can also be controlled using either the DualShock 2 controller or a USB mouse and keyboard.

Bonus material is available in the game, and the method of unlocking bonus material consists of shooting Memory Capsules, which are well hidden and found during the course of the game. Memory Capsules found during the story mode unlock the game's cutscenes, while a variety of Memory Capsules found in the Extra Missions mode unlock various other features, such as a music player, an artwork viewer, a character model viewer and additional extra missions.