“What has been covered up here?”
Wrong question.
Why did the Obama Administration make up a story out of thin air about a non-existent demonstration based on a video that probably fewer than 50 people in the Middle East had seen?
WHY THE LIE?
Then why hiding the truth?
Not actually true. There were at minimum some hundreds of rioters in Cairo storming the American embassy that same night.
While your basic point is valid, that the Benghazi attack was not a "protest" against the video, there is I would assume some possibility that the assault was initiated by people who were indeed offended by the video. Although this is probably unlikely due to the lag time to put together such an attack.