In Shogun: Total War you can hire both ninja and shinobi as strategic units.

The Tenno (read: all the player characters) of Warframe, who are essentially space ninjas with guns.

They come from a whole clan of ninja who defend Japan from evil spirits.

Soul Calibur also includes more 'traditional' ninjas in the form of Taki and her student, Natsu.

Theyre the ninjas who most represent the style of ninjutsu commonly seen in the media which is why they appeal to so many fans. Their techniques include fire breathing, imbuing their blades on fire, super speed, throwing teleporting kunais, etc.

Kunimitsu and her daughter are kunoichis whose style of ninjutsu is highly kinetic and full of spectacle.

He's, however, dowright appalled at Yoshimitsu's 'un-ninja' quirkiness and is quick to try to correct him.

Tekken also includes Raven, who's more a secret spy/agent with ninja stylings.

Tekken's Yoshimitsu is a ninja thief who has become a full-time cyborg over time, while the one from the Soul series is the mysterious leader of a band of thieves, and the last survivor of an actual ninja clan. They are far away from the common depiction, however, acting more like Samurais on crack.

Yoshimitsu appears in both the Tekken series and Soul Calibur, though Word of God states they're two different characters.

His allies are ninja, and he fights plenty of them.

Ninja Battle Heroes: The Player Character, Saizo, is one.

Shogun 2 kisho ninja