Kotaro's character is based off a renown ninja of the Hojo clan, Fuuma Kotaro, the leader a group of ninja from Sagami province. Unlike the Kotaro of the game who appeared to be a young novice ninja, Kotaro was supposedly a forty-year-old ninja leader when Onimusha 2: Samurai's Destiny takes place around 1573.
Although in all likelihood, as Kotaro was a name accepted by numerous heads of the Fuuma family, this Kotaro could have been intended as the son of the aforementioned man, especially considering his character arc's ending.