i just cant beat the ninja in the lab. i use chaff to get him to stop moving and then shoot him. i tried using explosives but they have no effect. but eventually run out of chaff grenades and have nothing to do. is there something im missing, like another way to attack him

Hi mate.
Its been a while since i played the game but i seem to remember that to defeat him you need to punch and kick him as your weapons don't harm him.
Just reinstalled the game and started playing it again so when i get up him again and kick his ass ill repost and tell you if using your fists is the way to beat him.
Hope this helps

yeah you do have to fight him in hand to hand combat ,hit him and he will put his sword away so then you just throw some Chaffs and you should beat him easily