Ninja Gaiden Sigma is a remake of Ninja Gaiden Black updated for the PlayStation 3 platform. The main storyline is the same, with the addition of a new playable character, Rachel, the demon hunter. She has 11 missions in the Mission mode (2 hidden) and is playable in 3 of her own chapters. She wields a warhammer, the Peluda Tail (a whip) for projectiles and Blades of the Ouroborus for ninpo. Whereas the main character Ryu unlocks costumes, there are 7 new hairstyles for her to acquire.

There are also some changes for Ryu. His reverse wind technique has been changed, he can run on water while floating and fight at the same time, he can shoot arrow in mid-air, and uses restoration items without going to the menu. There is one new weapon, Dragon's Claw and Tiger's Fang; a set of dual katanas, and the speargun has become a projectile weapon.

In general, the graphics have been fine-tuned for the PS3's high definition capability, some FMV sequences have become in-game cut-scenes, there are changes to item placement, encounters, story build-up, AI and damage, three new enemies (MSAT bikers, Mermen, Ghost Fires) and two new bosses (Garnov, Alternator). Players can also shake the SIXAXIS controller to increase the strength of ninpo being casted.