Last year on the day after U.S. forces killed Osama bin Laden, the group he founded was seen by some as on its last legs. No more. While under siege by drones in Pakistan and increasingly in Yemen, Al Qaeda not only received a new lease of life from the Arab Awakening, but has created its largest safe havens and operational bases in more than a decade across the Arab world. It’s not a popular movement, but its ideology, organization and lethal power promise to be a long-term challenge to the world.

Since President Barack Obama came to office in 2009, there have been almost 300 lethal drone strikes in Pakistan flown from bases in Afghanistan, most of which targeted Al Qaeda operatives. Along with the raid on Abbottabad, the offensive has decimated the group’s leadership in Pakistan, putting it on the defensive. Its new leader, Ayman Zawahiri, works from hiding and is fighting to survive.

But Al Qaeda is not alone. Allies in Pakistan, like Lashkar e Tayyiba, the group that attacked Mumbai in 2008, or the Afghan and Pakistani Taliban, are under little or no pressure. LeT and the Afghan Taliban, focused as they are on non-Pakistani targets, still enjoy Pakistani intelligence patronage, even as the ISI fights the Pakistan Taliban. The capacity of some of these groups, especially LeT, to cause global mischief, even provoke a war in South Asia between India and Pakistan, is undiminished. Three of the five most wanted on America’s terrorist list, Zawahiri, LeT’s founder Hafeez Saeed and Taliban leader Mullah Omar are in Pakistan. Only Zawahiri is hiding, the other two enjoy the ISI’s backing. Zawahiri, too, likely has powerful protectors.

Like the rest of the world, Al Qaeda was surprised by the revolutions that toppled dictators in Tunisia, Egypt, Libya and Yemen. Its ideology of violence and jihad was initially challenged by the largely nonviolent revolutionary movements that swept across North Africa and the Middle East. But Al Qaeda is an adaptive organization. It has exploited the chaos of revolutionary change to create operational bases and new strongholds from one end of the Arab world to the other.

In North Africa, Al Qaeda in the Islamic Maghreb, AQIM, a franchise of the Al Qaeda global terror organization, has successfully aligned itself with a local extremist group in Mali named Ansar al Dine, or Defenders of the Faith. Together they’ve effectively taken control of the northern two thirds of Mali. Now they’re destroying the Islamic heritage of the fabled city of Timbuktu, much as Al Qaeda and the Taliban destroyed Afghanistan’s historical treasures in the years before 9/11.

AQIM has long been among Al Qaeda’s weaker franchises. Created from an Algerian terrorist group in 2006, it had some early success blowing up the United Nations headquarters in Algiers, but for most of its existence it’s been confined to kidnapping Westerners traveling in the remote deserts of Algeria, Mali, Mauretania and Niger and other criminal enterprises. UK sources say it raised €50 million this way. This spring after a military coup in Mali, AQIM found a partner in Ansar al Dine, and together they swept out government forces from the north of Mali. Then the two turned on a Tuareg independence movement which had initially been their partner. Now they control a vast Saharan stronghold the size of Texas.

AQIM’s exact role in the murder of U.S. Ambassador Chris Stevens in Benghazi on 9/11’s anniversary is being investigated. Moroccan and French leaders are now labeling the new AQIM stronghold in Mali the gravest threat to regional stability in more than a decade.

The combustible mix of AQIM, Ansar al Dine and Tuareg rebels is complex and dangerous. All are well armed, thanks to looting Libyan depots after the fall of Muammar Gaddafi. AQIM has acquired weapons from Libyan caches that probably make it the best armed Al Qaeda franchise in the world today.
In Egypt another Al Qaeda jihadist stronghold is developing in the desert of the Sinai Peninsula, long a depressed and angry backwater in Egypt. After the revolution disaffected Bedouin tribes in the Sinai cooperated with released jihadist prisoners from Hosni Mubarak’s jails to begin attacks on security installations and the Egypt-Israel gas pipeline. The jihadists in the Sinai have pledged their allegiance to Zawahiri, and he has repeatedly endorsed their attacks on Israeli targets. Libyan weapons have also found their way into the Sinai.

In Yemen, Al Qaeda in the Arabian Peninsula has exploited the fall of Ali Abdallah Saleh’s dictatorship to take over remote parts of the south and east of the country. It lost control of several towns to government counterattacks this summer, but it struck back with deadly attacks on security targets in Sana’a, Aden and other major cities. AQAP has launched three attempts to attack targets in the United States since 2009 – only luck and good intelligence cooperation between the US, UK and Saudi Arabia have foiled them so far. Increasingly drones are attacking AQAP in the deserts of Yemen, killing operative Anwar al Awlaki and Inspire editor Samir Khan, both US-born. Awlaki still inspires – a Bangladeshi arrested last week for planning to bomb the Federal Reserve Bank in New York says he was a follower.

In Iraq the 2007 surge was supposed to destroy Al Qaeda’s franchise, the Islamic State of Iraq. Despite enormous pressure and repeated decapitation of senior leadership, the group has survived and recovered. It appeals to the Sunni Arab minority, which feels oppressed by the Shia-dominated government. Al Qaeda in Iraq focuses its attacks on the Shia regime, which it labels a modern “Safavid evil den,” a reference to the Shia Persian Empire in the 17th century that ruled Iran and Iraq. Its leader, Abu Bakr al Baghdadi, has promised more attacks in Iraq and in the United States.

Al Qaeda in Iraq is also working to export its jihad into the chaos and civil war in Syria. Zawahiri called for jihadists across the world to flock to Syria this spring to join the uprising against the Bashar al Assad regime and the Alawite minority that supports it. For Al Qaeda, Assad and the Alawis are a perfect target: Many Sunnis believe Alawis to be a deviationist sect of Islam akin to Shiism that should be suppressed. While Al Qaeda is a small part of the opposition in Syria, it brings skills in bomb-making and suicide operations.

Now jihadist websites are reporting every day that new Al Qaeda “martyrs” have died in the fighting in Damascus and Aleppo from Saudi Arabia, Palestine and Egypt. Reliable reports from journalists speak of bands of jihadists operating in the country with a loose affiliation to Al Qaeda and composed of Muslim fanatics from as far away as Pakistan, Bangladesh and elsewhere.

The longer the civil war in Syria goes on, the more Al Qaeda will benefit from the chaos and sectarian polarization. It will also benefit from the spillover of violence from Syria into Lebanon, Turkey, Iraq and Jordan that’s all but inevitable.

Al Qaeda’s success in capitalizing on revolutionary change in the Arab World comes despite a lack of broad popular support. It remains an extremist movement that appeals only to a small minority. But terrorism is not a popularity contest. Al Qaeda today is stronger at the operational level in the Arab World than it has been in years, and its prospects for getting even stronger are rich.