One of the most well constructed and documented pieces casting serious doubts and questions on the government's story line concerning the various "acts" of September 11, 2001 is Chaim Kupferberg's trilogy of writings.
Here is a link to Part I entitled The Propaganda Preparation for 911 :
It is a long piece, as are the other two parts, but RK.com highly reccomends all readers spend time reading and thinking about what Kupferberg details. The other two parts are accessible through links on the bottom of the page our link will take you to.
It is clear many of the questions Kupferberg raises have been completely ignored by the major news networks/outlets and only when the public at large demands real inquiry will they and, more importantly, the government begin to acknowledge the glaring discrepancies behind them.