If you start with the assumption that the "official story" is wrong the government would be the next most plausible culprit.

Which government? Almost all the major world powers have spy agencies that could've pulled it off. Russia would do it because of ex-Soviets holding a grudge. China would do it to strengthen their relative economic power. Israel would do it to ensure the US would continue backing their military. Most of the countries in the middle east, and half the countries in Latin America have grievances against us.

Lots of people acted strangely that day, but trustworthy information is hard to come by. More than anything else, 9/11 reminds me of the story of Alexander Litvinenko, which was in the news in 2006: Spy poisoned, accuses spy agency, spy agency denies it and accuses different spy agency, radioactive trail painted to someone's door, and you might as well roll a die to decide who to accuse, because very skilled agents have already destroyed the evidence.