An airplane hit the Pentagon on 9/11, not a missile.
The alternate conspiracy theory I heard on the Pentagon crash was centered around who flew the airliner into the Pentagon, not whether or not an airliner flew into the Pentagon.
It's not all that hard to believe that an airliner flew into WTC2, since just about everyone on the planet has seen footage from a dozen cameras which show a 767/757 hitting the tower. Four planes didn't reach their destinations, four impacts are noted.
As for the alternate conspiracy theory, there are only a few remotely relevant facts. They are centered around the lack of credible identification for the 19 passengers labelled as the terrorists.
- First fact: the Dulles airport video tapes purported to show part of the Flight 77 check-in lack the camera id and time data that should be present on any airport surveillance capture.
- Second fact: the tapes would have to be taken 30 minutes after sunrise, but appear to show bright sunlight and short shadows for people and cars outside the terminal.
- Third fact: the sounds that appear to be the terrorists on the radio are extremely short and badly distorted, leaving little chance for actual identification.
- Fourth fact: people made several phone calls from the first three aircraft before they crashed, but there has been no public release of information that they physically described the terrorists (as middle-eastern or arabic).
- Fifth fact: flight 77 hit the Pentagon in the most heavily reinforced and least populated part of the building, a side that was not on a direct track from takeoff to the Pentagon.
Personally, I find these facts insufficient to dispute the government's conclusions
- There's no compelling reason to doubt the motive or the opportunity of radical islamist hijackers on 9/11. The presented story of the hijackers successful in seizing the aircraft is less astonishing than any alternative explanation.
- All of the cases where the hijackers were supposedly spotted after 9/11 have been resolved as cases of confused identity (similar/same name) or simply bad original reporting.
- Flight 77 was hijacked well into the flight (unlike Flights 11 and 175). Even though the side of the Pentagon hit was not on a direct track from Dulles to the Pentagon, it is very close to a direct track from where the transponders were disabled to the Pentagon.
As for how the WTC buildings collapsed: I agree, it sounds strange that 1) all three of the collapsed buildings would fall mostly down into their foundations 2) at rates consistent with an unimpeded collapse and 3) the heavily reinforced WTC7 fell while WTC6 remained standing (WTC6 was between WTC7 and WTC1/2).
I don't have an explanation for what happened, but then, I'm not a structural engineer. According to the engineers I've read, however, there simply isn't enough information about the collapse of well-engineered steel structures to accurately predict how they should behave during collapse. I do recall, however, that during the collapse, the bottom of each tower looked normal (windows intact, etc.) until engulfed in the debris cloud. The bottom of the tower did not look anything like the "simultaneous collapse" that deliberate building demolition almost always resembles.
Further, I do know that a puddle of kerosene burning will burn at a much lower temperature than a properly aerated and driven kerosene torch (as in, I know from personal experience that you can run a steel forge on kerosene with a correctly sized blower to supply air to the flame) and so I find it highly credible that a kerosene fire could reach well past steel annealing temperatures and get to steel melting temperatures, depending on the specifics of fuel and air flow in the fire.
Ultimately, though, there's no reason to waste your time wondering if the government actually did the atrocities of 9/11 or if several decades of destructive US foreign policy and fanatical Islam together motivated the attacks. What's more important is how we respond as a country to 1) make sure that the US puts an end to decades of horrors perpetrated in yours and my name and 2) that in our pursuit of revenge for wrongs, we do not give up the freedoms and liberty which used to so clearly define this country.