Okay I assume you have the part of the rod you get from the diseased one's temple. You can't kill the unseeing eye without the completed rod. Are you in the unseeing eye's pit (where you go down past the ghoul town)? Okay the other bit of the rod is on the far right hand side, in a container. Once you get it the rod will complete itself then when you leave the room the unseeing eye will appear.
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