At the same time the Indonesian government, which at one point had denied that JI even existed, mounted a sophisticated campaign to dismantle the group, capturing many of its leaders and putting them on trial.
In the Philippines, the Abu Sayyaf Group, a number of whose leaders had trained in Afghanistan in al Qaeda's camps, and which specialized in kidnapping Westerners in the years after 9/11, was effectively dismantled by the Philippine army working in tandem with a small contingent of U.S. Special Operations Forces.
In Pakistan, the Pakistani Taliban in 2009 took over the once-tranquil mountainous vacation destination of Swat, and destroyed some 180 schools and beheaded 70 policemen there. Suddenly, they were only 70 miles from the capital Islamabad and some warned that the Pakistani state was in danger. Today, the Pakistani Taliban have been rolled back to their bases along the Afghan border and 16 of their leaders have been killed by CIA drones since President Obama took office.
Al Qaeda militants based in Saudi Arabia mounted a terrorist campaign beginning in 2003 that killed dozens of Saudis, and they also attacked a number of the oil workers and oil facilities that lie at the heart of the Saudi economy. This prompted the Saudi government to mount such an effective crackdown that the few remaining al Qaeda leaders who were not killed or captured have in recent years fled south to Yemen where the remnants of al Qaeda in the Arabian Peninsula (AQAP) are now based.
From its new headquarters in Yemen AQAP has made serious efforts to attack the United States, sending the "underwear bomber" to blow up Northwest Flight 253 over Detroit on Christmas Day 2009 and also smuggling bombs on to U.S.-bound cargo shipments in October 2010.
None of these attempts were successful.
Yemen militants decimated
As a result of the threat posed by AQAP, the United States has mounted a devastating campaign against the group over the past three years. There was one American drone strike in Yemen in 2009. In 2012 there were 46. That drone campaign has killed 28 prominent members of the group, according to a count by the New America Foundation. Among them was the No. 2 in AQAP, Said al-Shihri, who was confirmed to be dead last week.
In the chaos of the multiple civil wars that gripped Yemen in 2011, AQAP seized a number of towns in southern Yemen. But AQAP has now been pushed out of those towns because of effective joint operations between U.S. Special Operations Forces, the CIA and the Yemeni government.
The Yemeni president, Abd Rabbuh Mansur Hadi, even went to the United Nations General Assembly in September where he publicly endorsed the use of CIA drones in his country, something of a first.
A couple of years ago, al Qaeda's Somali affiliate, Al- Shabaab ("the youth" in Arabic) controlled much of southern Somalia including key cities such as the capital Mogadishu.
Once in a position of power, Shaabab inflicted Taliban-like rule on a reluctant Somali population, which eroded its popular legitimacy. Shabaab was also the target of effective military operations by the military of neighboring Kenya, troops of the African Union and U.S. Special Operation Forces.
As a result, today the group controls only some rural areas and for the first time in two decades the United States has formally recognized a Somali government.
Mali conflict shows weakness of jihadist militant groups
Similarly, groups with an al Qaeda-like agenda captured most of northern Mali last year, a vast desert region the size of France. Once in power they imposed Taliban-like strictures on the population, banning smoking and music and enforcing their interpretation of Sharia law with the amputation of hands. The militants also destroyed tombs in the ancient city of Timbuktu, a UNESCO World Heritage site, on the grounds that the tombs promoted "idol worship."
None of these measures endeared the jihadist militants to the population of Mali. In the past weeks, as a relatively small force of some 2,000 French soldiers has rolled through Mali putting the militants on the run, the French have been cheered on by dancing and singing Malians.
When French soldiers are greeted as an army of liberation in an area of the world that in the past century was part of a vast French empire, you can get a sense of how much the jihadist militants had alienated the locals.
Last week the French military took the city of Timbuktu. The defeat of the al Qaeda-linked groups as effective insurgent forces in Mali is now almost complete.
What has just happened in Mali gets to the central problem that jihadist militant groups invariably have. Wherever they begin to control territory and population they create self-styled Islamic "emirates" where they then rule like the Taliban.
Over time this doesn't go down too well with the locals, who usually practice a far less austere version of Islam, and they eventually rise up against the militants, or, if they are too weak to do so themselves, they will cheer on an outside intervention to turf out the militants.