A counter-factual question raised by RUSI's Shashank Joshi, so hat tip to him. What if Pakistani nuclear weapons had been present in Afghanistan in September 2001? Ridiculous idea, but he has found this unsupported WaPo report from November 2001:
Pakistani fears of an Indian attack on its nuclear sites were so great in the summer of 1999, after Pakistani-supported guerrillas invaded Indian territory, that military officers here secretly contacted Taliban officials about the possibility of moving some nuclear assets westward to neighboring Afghanistan for safekeeping, according to a recently retired Pakistani general officer familiar with the talks.

”The option was actively discussed with the Taliban after some indications emerged that India may open hostilities at the eastern border,” the retired official said. ‘‘The Taliban accepted the requests with open arms.”

The former official said the talks were ”exploratory” and said that no nuclear-related assets were placed in Afghanistan. At the time, Pakistan’s military and intelligence services had close relations with the Taliban, providing training, weapons and other support.
Link to WaPo:http://www.recordnet.com/apps/pbcs.d...NEWS/311119943 and Shashank's blog:http://shashankjoshi.wordpress.com/2...is-that-wasnt/

Speculate away! I've added this comment to the blog:
What if the nuclear weapons had been present in Afghanistan in September 2001?

A lot depends on how many knew they were in country, whether in Kabul, Delhi, Islamabad, Tehran and Washington. More particularly how many knew exactly their location(s).

For a moment let us assume others only knew after 9/11. In the heated atmosphere, in the USA and beyond it is easy to speculate that the USA would have struck first if the targets had been identified. Even today a vague sign that AQ plus have a WMD intention sends the USA into hyper-drive, let alone has a capability.

Pakistan I expect would have swiftly withdrawn any such weapons and signalled that clearly to “interested parties”. Adding it had been a low-level decision and was a big mistake.

Hopefully those “far more in the know” can answer.