The Black Ninjas are the enemies of the White Ninjas (and the rest of Takoshima City) and are allied with the KGB. Crypto convinces them to worship Arkvoodle after telling them that Arkvoodle is better than the evil God "Darkvoodle". Nevertheless, for some unknown reason they still attack Crypto.
According to the White Ninja Leader, the two factions of Ninja were originally one, and wore grey. After the death of the Grey 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, beating the future White Ninja faction who also desired black clothing. Since then, the two have continued to drift apart, the White Ninja focusing on spiritual matters, the Black Ninja drifting to activities such as law-breaking, robbery, criminality and terrorism.
According to one Takoshimese man, a large part of their appeal is that, unlike the White Ninja, they get paid.
The Black Ninja are, without a doubt, the most aggressive human faction in the game. With the exception of the KGB, all Black Ninjas seen in the game will attack all others on sight (including civilians, cops, soldiers, Crypto, and of course their enemy the White Ninjas), and, in return, Cops, Soldiers and White Ninjas will attack them on sight.
In regards to combat strategy, they use similar tactics as the White Ninja. They move around very quickly, throwing blades at their enemies, and can teleport in clouds of black smoke.