That the Alliance was a real threat to the Taleban was underlined when, two days before the attacks occurred in New York and Washington DC, the Alliance's charismatic leader for 25 years, Ahmad Shah Massoud, was killed by suicide bombers posing as journalists.
Having started the Alliance back in 1979 to foster resistance against the invading forces of the USSR, he was renowned among the Russians as one of the best mujahedin commanders. He was dubbed by the Afghans the Lion of Panjshir, the name of his valley 64km north of Kabul.
Yet the record of Massoud's mainly Tajik-dominated Northern Alliance was so bad in the years that they held Kabul (1992-96), that the desire by the local population for peace and order was one of the reasons they lost it to the Taleban.
Kabul was destroyed by rocket attacks during these years, after the Russians had pulled out and as different commanders of the Northern Alliance fought among themselves for control of the city.
Many of the commanders were little more than oppressive warlords. Armed by outside interests (Iran, Russia, India and the central Asian republics), these men developed their own fighting forces or factions and often switched sides in battle, depending on which outside interests could pay them most.
One of the cruellest of these Northern Alliance commanders was Abdul Rashid Dostum, an Uzbek. He is now waiting in the wings to fight alongside US forces against the Taleban. But during the early 1990s, his forces committed many atrocities against the population of Kabul, including widespread rape.
A spokeswoman, named only as Fatima, for an organisation describing itself as the Revolutionary Association of the Women of Afghanistan says: "The Northern Alliance are the second Taleban. They are hypocrites; they say they are for democracy and human rights but we can't forget the black experience we had with them.
"Seventy-year-old grandmothers were raped during their rule; thousands of girls were raped. Thousands were killed and tortured. They are the first government that started this tragedy in Afghanistan."
Another Northern Alliance commander, Rasoul Sayaf, a Pashtun, ran the Union for Freedom of Afghanistan, yet his men were also implicated in the use of Shia women as sex slaves during the Alliance's reign in Kabul.
Another, Gulbuddin Hikmetyer, a Pashtun, had an ongoing feud with Massoud and it was their rivalry that prevented the formation of a Pashtun/Tajik alliance, an arrangement that might have prevented the country from being taken over by the Taleban in 1996.
By 1996, the Alliance had managed to coalesce into an agreement between Massoud, Dostum, and the Hazara leader Karim Khalili.
They set up the Supreme Council for the Defence of the Motherland and have continued to oppose the Taleban, but their ability to stay united has not been matched by any great military success.
The main components are Dostum's Uzbek Junbish-i-Milli-yi Islami, Khalilli's Hazara Shia groupings of the Hizb-i Wahdat and the Tajik Jamiat-i-Islami, led by Massoud's successor, General Mohammed Fahim Khan.
They are committed Muslims but lack the Taleban militancy. In their heartland of Faizabad women can work and girls can gain higher education, although their record in Kabul does not inspire confidence in their respect for human rights.
This week White House spokesman Ari Fleischer repeated the American line. "We do not want to choose who rules Afghanistan, though we will assist those who seek a peaceful, economically developing Afghanistan, free of terrorism."
It is difficult to argue that the Northern Alliance meets that job description. But the vacuum will have to be filled or anarchy will again provide the breeding ground for terror.
* Additional reporting by agencies
Map: Opposing forces in the war against terror
Afghanistan facts and links
Full coverage: Terror in America