The gameplay for Sigma is very similar to the original version, albeit with some modifications made to the game. Like the original version, the player's movements and combat system are directed using the console gamepad, which comprises the left thumbstick, two attack buttons, and a block button. The game features a large selection of weapons for Ryu to wield each with advantages and disadvantages that affect the way the player approaches combat. A new addition to Ryu's arsenal is a pair of dual-wield swords, Dragon's Claw and Tiger's Fang. It also provides Ryu with magical spells in the form of ninpo, which allows him to inflict heavy damage on enemies while potentially avoiding damage himself. By shaking the Sixaxis controller, players are able to increase the power of their ninpo spells. Rachel, a non-playable character in the 2004 game, became playable in three new chapters, featuring the new bosses, Gamov and Alterator. Some of the design elements of the old levels was also changed and several new enemy types were introduced.

In addition to the narrative Story Mode, Sigma included a gameplay variation called Mission Mode. Focused on action rather than character development, this provides combat-based missions set mainly in small areas. In both Story and Mission modes, game scoring is based on the player's speed in clearing encounters, the number of kills achieved, the number of unused ninpos remaining at the end, and the amount of cash collected. Players can compare their scores on online ranking boards. In addition, players have the option to customize the appearance of player characters, with selectable costumes for Ryu and hairstyles for Rachel.