There are many 9/11-related threads on this site, but I don’t think I’ve seen this scenario discussed. First, some background:

https://www.tandfonline.com/doi/abs/10.1080/09592318.2014.945634?src=recsys&journalCode=fswi20
In 1989 the Soviet Union withdrew its forces from Afghanistan leaving the embattled Afghan Communist government of President Mohammad Najibullah to fight against an emboldened mujahideen insurgency. Most experts expected a quick mujahideen victory once the Soviets were no longer directly involved in counterinsurgency operations in support of the Afghan government. But in the spring of 1989 the Afghan Communists beat the odds and defeated a mujahideen rebel offensive designed to capture the eastern city of Jalalabad. This proved to be a turning point, and for the next three years the Najibullah regime held out against the mujahideen ‘freedom fighters’. In fact the Afghan Communist regime actually outlasted its sponsor the Soviet Union. The reasons for this remarkable achievement can be traced, in part, to ethnic–tribal divisions among the quarreling mujahideen parties and the Afghan government's ability to exploit them.
In the end, the Communist government lost the civil war in the 1990s in no small part because Yeltsin’s Russian government cut off food and fuel aid it was providing to Kabul.

Now let’s discuss a hypothetical timeline where Yeltsin and his advisers decide that continuing to supply Najibullah government with fuel and food serves Russia’s interests. Najibullah‘s government doesn’t collapse and the war ends in a draw — Kabul, through both force of arms and reconciliation is able to hold on to northern Afghanistan but lacks the power to hold onto the Pashtun areas next to Pakistan. Sure, Kabul claims that they are part of Afghanistan, but de facto “Pashtustan” is a Taliban-controlled, Pakistan-backed break-away Wahhabist state.

The Taliban still give refuge to Osma Bin-Laden and Al-Qaeda and they still perform a 9/11-like attack on USA around the year 2001 (and to make things simpler, yes, let’s assume G.W. Bush is still president in this ATL)

What would the American leadership do now? Would they ally with Najibullah (or whomever is his successor) after supporting the opposing side for so long? How would it go down with the US public/America’s Middle East allies, especially if the Kabul government is still at least nominally communist? Would Najibullah/his successor even agree to join forces with USA against the Taliban if Washington made that offer?

If US doesn’t ally with communist Kabul does it do something stupid like declaring war on both the Afghan government AND the Taliban at the same time? Or does it claim that the 9/11 attacks were organized by Al-Qaeda on orders from Afghan communists?
 
What would the American leadership do now? Would they ally with Najibullah (or whomever is his successor)
Yes

How would it go down with the US public/America’s Middle East allies, especially if the Kabul government is still at least nominally communist?
wouldn't give shit since that cold war is over
Would Najibullah/his successor even agree to join forces with USA against the Taliban if Washington made that offer?
Yes
 
It all turns on if a communist Afghanistan would give sanctuary to Osama. Which I seriously doubt.
If Afghanistan isn’t giving shelter to Osama after he was kicked out of Sudan; then where would he wind up?
If he is in Afghanistan on 9/11, even if the Cold War isn’t over, the Russians/Soviets are going to tell the Afghans they are on their own.
 
Okay, I just read the ENTIRE POD.
The US would ally w/ Kabul in this case. If Kabul decides to fight the US the Russia will ask Kabul WTF is wrong w/ you & tell them they are on their own.
 
Both Nato and the Warsaw Pact would hunt him down. A dangerous loose cannon like that could start a war that could get EVERYONE killed. Any nation that shelters him will be toast.
 
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