Why did the third plane on September 11 hit the pentagon?

Because the Al-Qaeda terrorists who hijacked the plane, took the controls and intentionally flew the commercial passenger jet into the Pentagon because it is the Headquarters for the U.S. Department of Defense. The hijackers intended to strike a blow at, or even cripple America's military, and hit key targets that represented America's strength world-wide. It is likely that the terrorists also wanted to instill fear in Americans by showing that they could be hit, even at such an allegedly secure facility.