Here's a quick draft of my alternative theory which I look forward to posting very soon everywhere!
The components of the theory 1.) Putin's rise to power and the Moscow apartment bombings. False flag model for Islamic terrorism. A small scale "proof of concept" for 9/11. The seed which Putin's political career was spun around, and continues to be; a combination of misinformation, Islamic persecution, nationalistic anti-Western propaganda, military action, and dictatorial power derived from false crisis.
2.) A. Litvinenko and I. Pacepa claim that Al Qaeda second in command Ayman Al-Zawahiri is a KGB agent who received training in Baluchistan. Further, they claim that Islamic terror has been a prinicpal tool of the Russian intelligence services since the 1970s. The goal of the campaign is to utilize the similarities between Islam / Orthodox Christianity and Islamism / Communism to create new mid-east states in the Soviet Union's sphere of influence, discredit Israel and the USA (Stalin/Russia having felt betrayed that for their initial support Israel sided with the US) and make them the enemies of Muslims, as well as provide a platform for asymmetric/plausibly deniable warfare which does not justify a nuclear retaliation. A common theme echoed by Pacepa and Litvinenko is that the Soviet Union had a common tactic of using disinformation in order to provoke or cause their enemies to act in their interest. An overarching theme according to Pacepa was turning Islamic forces against Israel and the US (some say Stalin harbored resentment to Israel for principally siding with US) by manipulating long held biases. At one time, the KGB employed 4000 operatives across the middle east, spreading anti zionist propaganda like Protocols of the Elders of Zion among the people. The failure / collapse of Russia's conventional military strategy in Europe necessitated that they find new grounds to maintain strategic parity with the US.
3.) Following the fall of communism, Russia may have manipulated newly forged strategic ties with America to mislead intelligence/military planners. A. this includes the generally unprecedented Russian air exercises which had engaged NORAD on 9/11, far north of the continental US., B. Russian overtures of intelligence support and warnings of suicide pilot threats leading up to 9/11 -- framing the Islamists before the attacks even happened, C. It is reasonable to assume high level connections between the legacy components of the Bush administration under GHW Bush and therefore GW Bush's similarly composed administration and Putin's government, derivative of Yeltsin's -- which GHW Bush had been involved in establishing at the fall of communism. We can assume some high level "face value" trust in the (naive?) exuberance following the jubilant fall of communism. GW Bush's administration therefore became the perfect pawn for Putin in order to manipulate. Putin was the first to call Bush on 9/11 and ostensibly "build trust". D. The Bush administration's pre-existing beliefs about the regime of Saddam Hussein for example made middle east action inspired by world events easier for Russia to manipulate. It would seem highly plausible that Russian misinformation was fed to the Bush administration which justified their biases against Saddam and led them to war in Iraq (again the financial destruction * backfire strategy * make Islam hate US = motivation) 4.) Putin was jealous of America's continued success and unprecedented, seemingly unpoppable tech bubble following the fall of communism. While America continued to rise, Russia continued to fall behind. The attack was jealously designed to cripple our economy. A. It caused outright damage to the critical financial institutions, dealing a critical structural blow to the ability of those institutions to physically operate; as well as rendered much of the prinicipal financial district unusable. A sharp drop in stocks came shortly after., B. it drew America into an extremely costly conflict in Afghanistan (a warzone that had nearly bankrupted the Soviets while fighting US-backed Muhajeddin decades earlier -- is it so obvious a reprisal. The Russians may have considered it unwinnable quagmire). The combination of unplanned long and costly war, America's growing debt, and stock market meltdown may have contributed to the timing of this attack. C. Possible misinformation leads Bush administration into Iraq.
Get ready for round 2. Since they obviously failed on 9/11, they're up to their old Al-Qaeda tricks again with ISIS.