According to the White Ninja Leader, the two factions of the Ninjas were originally one, and wore gray. After the death of the Gray Ninja Master, the two factions split: the main reason for the schism along black and white lines was not because of moral, political or ideological reasons, as Crypto initially thought, but because the Black Ninjas got their order for black fabric in first and beat the future White Ninjas who also desired black clothing. Since then, the two continued to drift apart, the White Ninjas focused on spiritual matters and the Black Ninjas drifted to activities such as law-breaking, robbery, criminality, and terrorism.
According to one Takoshima man, a large part of the Black Ninjas appeal was that, unlike the White Ninjas, they got paid. Crypto convinced the Black Ninjas to worship Arkvoodle after he told them that Arkvoodle was better than the evil God, "Darkvoodle". Nevertheless, for some unknown reason, the Black Ninjas still attacked Crypto.
The Black Ninja were, without a doubt, the most aggressive Human faction in the game. With the exception of the KGB, all Black Ninjas who were seen in the game attacked all others on sight (including civilians, Cops, the Army, Crypto, and of course, the White Ninjas), and, in return, Cops, the Army, and the White Ninjas attacked them on sight.
In regards to combat strategy, the Black Ninjas used similar tactics as the White Ninjas. They moved around very quickly, threw blades at their enemies, slashed with their claws and swords, and teleported in clouds of black smoke.