Some planes took off with people on them who were never seen again, and some planes hit some buildings (not the Pentagon though). Plane impact/Jet fuel fires did not bring down the WTT.
Various elements of the Bush Administration/CIA/Pentagon (+ others?) planned/assisted the events (utilizing their "mujahideen" database for scapegoats), and then covered it up and seized the opportunity to expand the war/spook departments, create extreme domestic controls, and destabilize the geopolitical landscape in the middle east in the West's favor.
The means, motive, and opportunity were all present for the Bush Administration (which had generational ties to the CIA/DoD). There was at best, a questionable motive for "islamic operatives" attacking the WTC, and no means or opportunity without inside help.