If you shoot all 64-some odd number of the Kerotan frogs you get a special camo. They carry over to the next game, so you don't have to go back and get the ones you've already gotten again when you start a new game.
Killing the bosses with the tranq only lets you get their camos.
You can't CQC the Boss because she is the master of it. The only time it works on her is while she is grabbing you, mash the buttons, and 90% of the time you'll counter her and you'll get a free shot.
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