"Why this happened" should be considered separately from the science. Having said that, your question is still valid:
I, as well as many others, have possible, if not reasonable explainations as to why Dr. Jones' hypothesis would be true.
However, once these ideas are brought into the discussion, emotional attachments to preconceived notions tend to cloud judgement. - hence my reservations in discussing why... not to mention that this discusion is more indefinite than considering the physics of the issue ...
But since this is your question, I will answer it by saying the events of 911, in many ways, seem to be a classic case of the problem-reaction-solution paradigm (Hegelian in nature) that has been a normal, although mostly unnoticed, part of human history. Having said that, I would like to add again that my speculation here is merely a hypothesis and should be considered separately from quantitative data.
This information is touches on the paradigm I described above:
Operation Northwoods documents are very important to this issue (3 links provided below text):
Operation Northwoods or Northwoods was the code name for various false flag actions, including domestic terror attacks (such as involving the use of "hijacked" planes) on U.S. soil, proposed in 1962 by senior U.S. Department of Defense leaders to generate U.S. public support for military action against Cuba. The proposal was presented in a document entitled "Justification for US Military Intervention in Cuba," a draft memorandum pdf) written by the Department of Defense (DoD) and Joint Chiefs of Staff (JCS) representative to the Caribbean Survey Group. The draft memo was presented by the JCS to Secretary of Defense Robert McNamara on March 13 with one paragraph approved, as a preliminary submission for planning purposes. However, McNamara rejected the proposal. In addition, the existence of Operation Northwoods was often dismissed by the general U.S. public as an unfounded "conspiracy theory" until the draft memorandum was declassified in recent years through a Freedom of Information Act request by the National Security Archive.
http://www.whatreallyhappened.com/northwoods.html
http://en.wikipedia.org/wiki/Operation_Northwoods
http://www.gwu.edu/~nsarchiv/news/20010430/
Also:
http://www.propagandamatrix.com/diocletian.html
More examples:
Nero Claudius Caesar (37-68 CE) - (University of Texas History Deparment) - In 64 C.E., a fire swept through Rome, burning for a week and destroying a large portion of the city... According to some sources, when he found that he did not have enough land to build his palace, he set fire to the city a second time. It is at this point that he is said to have "played his fiddle [lyre] while Rome burned." To avert suspicion, he blamed the fires on the Christians and proceeded to kill them in horrendous ways.
Neither human effort nor princely largesse nor divine appeasement was able to dispel the scandal that the fire (which burned much of Rome in 64 CE) was believed to have been commanded (by the emperor Nero). So, to do away with the rumor, Nero substituted as culprits those who were commonly called "Christians," who were hated because of their absurdities. And he inflicted them with the most extraordinary punishments
The USS Maine Sank in Havana Harbor Launching the US into the Spanish American War
Sinking of the USS Maine Resulting in the Spanish American War - US Navy Official Website - The Spanish-American War (21 April to 13 August 1898) was a turning point in the history of the United States, signaling the country's emergence as a world power. The blowing up of the battleship USS Maine in Havana harbor on the evening of 15 February was a critical event on the road to that war... The U.S. Navy Department immediately formed a board of inquiry to determine the reason for Maine's destruction... When the Navy's verdict was announced, the American public reacted with predictable outrage... The destruction of Maine did not cause the U.S. to declare war on Spain, but it served as a catalyst, accelerating the approach to a diplomatic impasse. In addition, the sinking and deaths of U.S. sailors rallied American opinion more strongly behind armed intervention...Technical experts at the time of both investigations disagreed with the findings, believing that spontaneous combustion of coal in the bunker adjacent to the reserve six-inch magazine was the most likely cause of the explosion on board the ship. In 1976, Admiral Hyman G. Rickover published his book, "How the Battleship Maine Was Destroyed". The admiral became interested in the disaster and wondered if the application of modern scientific knowledge could determine the cause. He called on two experts on explosions and their effects on ship hulls. Using documentation gathered from the two official inquiries, as well as information on the construction and ammunition of Maine, the experts concluded that the damage caused to the ship was inconsistent with the external explosion of a mine. The most likely cause, they speculated, was spontaneous combustion of coal in the bunker next to the magazine. As a result (of the Spanish American War) Spain lost its control over the remains of its overseas empire -- Cuba, Puerto Rico, the Philippine islands, Guam, and other islands - Library of Congress - On April 25, 1898 the United States declared war on Spain following the sinking of the Battleship Maine in Havana harbor on February 15, 1898. The war ended with the signing of the Treaty of Paris on December 10, 1898. As a result Spain lost its control over the remains of its overseas empire -- Cuba, Puerto Rico, the Philippine islands, Guam, and other islands.
Events moved swiftly after the explosion aboard the U.S.S. Maine on February 15. On March 9, Congress passed a law allocating fifty million dollars to build up military strength. On March 28, the U.S. Naval Court of Inquiry finds that a mine blew up the Maine. On April 21 President McKinley orders a blockade of Cuba and four days later the U.S. declares war.
Adolf Hitler was elected Chancellor (President) and then Burnt the Reichstag (German Parliament) Building. He Then Declared Himself Furor (Dictator) and Promised Utopia. Hitler Declared Martial Law and Suspended All Basic Human Rights.
Reichstag Fire - Encyclopedia Britannica - Reichstag fire, burning of the Reichstag (parliament) building in Berlin, on the night of Feb. 27, 1933, a key event in the establishment of the Nazi dictatorship and widely believed to have been contrived by the newly formed Nazi government itself to turn public opinion against its opponents and to assume emergency powers...his propaganda minister, Joseph Goebbels, is supposed to have devised the scheme... On Feb. 28, 1933, the day after the fire, Hitler's dictatorship began with the enactment of a decree "for the Protection of the People and the State," which dispensed with all constitutional protection of political, personal, and property rights.
Hitler and the Reichstag Fire - (The Columbia Encyclopedia, Sixth Edition. 2001 - In Jan., 1933), when Adolf Hitler became chancellor without an absolute majority, the Reichstag was dissolved and new elections were set for Mar. 5; a violent election campaign ensued. On Feb. 27, 1933, a fire destroyed part of the Reichstag building. Hitler immediately accused the Communists of having set the fire. President von Hindenburg proclaimed a state of emergency and issued decrees suspending freedom of speech and assembly.
Holocaust Timeline The Nazification of Germany - University of South Florida - On February 27, 1933, the Reichstag building went up in flames. Nazis immediately claimed that this was the beginning of a Communist revolution. This fact leads many historians to believe that Nazis actually set, or help set the fire. Others believe that a deranged Dutch Communist set the fire. The issue has never been resolved. This incident prompted Hitler to convince Hindenburg to issue a Decree for the Protection of People and State that granted Nazis sweeping power to deal with the so-called emergency. This laid the foundation for a police state.