Is he in their barracks? The quest I got to kill him says hes in the rainforest ancient ruins, but I searched the whole thing...the only boss there is Slayer X and there's 1 plunderer elite
Yes, he is is the plunderer pyramid. You will fight a chief elite, and then the leader should be the last boss you get to. Your quest does it list a specific name or just plundered leader?
