So I'm on the last level. Because of those 16 ninjas at lv 48, I lost 3 gems. THREE. Nothing could penetrate through my defenses cept for those guys, of how I hate them...;-;
IM WITH YOU!!! Them and their invisibility thingy! The first time they spawned in the game I wasn't paying attention and when my towers weren't shooting them I was like WTF!!!
Two ways to counter them. If you can get a Ballista tower high enough, it can 1-shot the Ninjas before they drop their smoke bomb. The other is to make sure you tag them fast enough that they can be invisible for 5 seconds and you can still take them out before they reach the gems. It is a little nerve wracking on the last level, but I've done it.
If all else fails, drop a meteor. The wave 40 boss on the last level is pretty simple if you drop four, 400 damage meteors on his head.
The second to last level has the hardest Ninja with 2500 HP. You HAVE to fear him or freeze him with your first shot or bye-bye brilliant.