Akai Hayate

Japan is secretly controlled by a tyrannical group of ninjas called the Shinogara. Their finest assassin is a man named Hayate Kanuma, whose father leads the Shinogara. Hayate, however, knows that the secret society's control over Japan is wrong. Sacrificing his own safety, Hayate kills his father. Now he's on the run, safe almost nowhere from his vengeful former comrades except perhaps for the one hiding place he decides upon: his sister. (myanimelist.net)