-Put away your weapon and punch him instead. He will jump away from you and put away his weapon. Throw more punches at him and he will turn invisible and hide. Toss a chaff grenade to stun him and then use your Fa-Mas/SOCOM to hurt him. Keep doing this until he is dead. Note strategy: He may take out his weapon again if you use yours. When his health is gone, a force field will surround him. Aim at him and shoot. You will have to do this three times.
-After the fight, when the Ninja is surrounded by the energy field, you can use any desired weapon instead of finishing him off with three punches.
-After he loses his sword in Octacon's lab, toss chaff grenades. He will stop and you can run up to hit and kick him. You have to be quick because he will kneel down in about seven seconds and wait for it to clear. After you kick and hit him, he will also kneel down.