Here are a few questions to consider:
1. A record number of "put options" (bets that the price of a stock would drop) were placed just prior to 9-11 on American Airlines, United Airlines, and Morgan Stanley (who leased 22 floors in the World Trade Center (WTC). The CIA monitors stock trading in real-time. Many of these "put options" have been traced back to the investment firm of A. B. Brown-Deutche Bank. Trades cannot be placed anonymously, so why hasn't the CIA, FBI, or the SEC investigated these transactions further and determined who purchased these put options? Who is this person and how did they have prior knowledge of the attacks?
2. Why didn't the 9-11 Commission mention the Air Force wargames on 9/11: Vigilant Guardian, Vigilant Warrior, Northern Guardian, Northern Vigilance, and the fact that they drew most of the air defense away from the East Coast region on that day?
3. If the 9-11 Commission actually had been informed of the Able Danger project (tracking the terrorists, including Mohammed Atta) several times, why wasn't any of that covered in their report?
4. Former FBI translator Sibel Edmonds gave three and a half hours of behind closed door testimony to the 9-11 Commission. Why did the Commission only write one sentence about her testimony (in a footnote) and why is she under a gag order not to talk about what she knows?
5. Why did President Bush tell the FBI to back off investigating both the Saudi government and the bin Laden family in early 2001?
6. In the first Congressional Report on 9-11, why were 28 pages covering the subject of Saudi Arabia and their ties to funding terrorist groups redacted from the final report?
7. There were multiple conflict of interest issues involving most (if not all) of the 9-11 Commission members. From their ties to the CIA, Saudi Arabia, and the Bush administration to investments in the oil industry. Why were such clearly heavily biased insiders chosen?
8. Why was President George W. Bush allowed to remain in the elementary school after Andrew Card whispered to him that the second WTC tower had been struck and that "America was under attack"? Why did Mr. Bush remain sitting in the classroom and continue to listen to children reading a book after he was informed? Why didn't he immediately leave to contact the Pentagon and direct NORAD to alert fighter jets to fly a protective perimeter over NYC and Washington and to intercept all hijacked airliners? Why were no fighter jets scrambled until about 90 minutes after the first plane (Flight 11) was identified as being hijacked?
9. Why didn't the Secret Service immediately take Mr. Bush out of danger to a safe place? If America was under attack and two planes had already crashed into the Twin Towers, why did the Secret Service feel the President was safe in a public school building? His trip to the Booker Elementary School was well publicized to the general public and media.
10. How was Flight 77 allowed to continue on it's course towards Washington D.C. while Vice President Dick Cheney sat in the President's Emergency Operations Center (PEOC) and was informed of it's direction and given reports about the plane being 50 miles out, 30 miles out, 10 miles out? The Pentagon is armed with anti-aircraft batteries surrounding the entire complex. Why were no defensive measures taken?
11. What happened to all of the flight recorders of the four hijacked planes that day? Why has the information within been suppressed?
12. Why did the 9-11 Commission completely refuse to explain the destruction of WTC building #7? How could FEMA's investigation of the destruction of WTC #7 result in their issuing a statement saying that "The collapse of WTC #7 remains unknown at this time?"
13. In the PBS documentary entitled "America Rebuilds", WTC leaseholder Larry Silverstein admits on camera that they decided to "pull" (meaning "implode by controlled demolition") WTC building #7. WTC #7 only had isolated pockets of fire on floors 7-12. How can a 47 story building be set up to implode in a matter of a few hours? To perform a controlled demolition, this requires a complete structural analysis of the building and explosives must be placed at the lower support column infrastructure.
14. Why was Silverstein's claim not investigated?
15. If Flight 93 was brought down in a crash in Shanksville, PA by a struggle between the hijackers and passengers on board, what explains a debris field of wreckage that covered an area of between a 5 to 8 mile radius? Multi-ton aircraft engines don't bounce miles away from the site of the initial impact. Why was there no visible debris from the crashed airliner at the crash site, and no human remains of the passengers and crew?
16. Why was the debris from the collapsed Twin Towers immediately loaded on to trucks and put on freighter ships to Asia to be melted down? It is a federal offense to remove material from a crime scene.
17. The official explanation is that the Twin Towers collapsed based on the so-called "pancake theory". The towers could not have collapsed in the 8.4-10 seconds that they did (virtually free-fall speed), since if one floor was striking another floor beneath it, each floor would encounter resistance and slow down the collapse. There are ample amounts of video and audio that document the eyewitnesses (survivors, fire fighters, policemen etc.) who recall hearing explosions going off right before the towers fell.
18. It is odd that all three WTC buildings (1, 2 and 7) totally collapsed on that day. Never before or since in engineering history have steel structure high rise buildings completely collapsed due to fire.
19. Why did President Bush agree to answer questions from the 9-11 Commission only if he was accompanied by Vice President Cheney? Why did they stipulate that no audio or video recordings be allowed in this interview? Also, no notes or transcripts of this event were allowed and both the President and the Vice President refused to testify under oath.
And this is only a partial list...