Al-Qaeda has staged a remarkable comeback in Iraq in the last year. Former National Security Advisor Jim Jones has called it “al-Qaeda’s renaissance”. Al-Qaeda could stage another renaissance in South Asia if the American drawdown from Afghanistan is botched.

The rise of al-Qaeda affiliates in the fertile crescent from Beirut to Baghdad has been dramatic. Al-Qaeda in Iraq, once wrongly proclaimed defeated by many, has regenerated, more deadly than ever, as the Islamic State of Iraq and al-Shams (ISIS). Today, it is fighting to once again take control of the Anbar province. It has already successfully given birth to a Syrian franchise, the al-Nusra Front, and now competes with its own offspring for power in Syria. Together, the ISIS and al-Nusra are trying to destroy the century-old borders of the region, tearing down the hated Sykes-Picot borders drawn by London and Paris in the aftermath of World War I. Thousands of jihadis from across the Muslim world, many from Europe, have already flocked to Syria to join the fight against President Bashar al-Assad’s regime. Sunni-Shia sectarian violence is multiplying, feeding a fire that al-Qaeda has long stoked.

Al-Qaeda’s Lebanese franchise, the Abdullah Azzam Brigades, is trying to import the Syrian civil war into Lebanon. Named after the Palestinian ideologue who was Osama bin Laden’s key partner in Afghanistan in the 1980s, the Abdullah Azzam Brigades took credit for the attack on the Iranian embassy in Beirut last November and have been linked to other car bombings since. The death of its leader, Majid bin Muhammad al-Majid, a Saudi Arabian, is not likely to put an end to its efforts.

There was no al-Qaeda in Iraq before 9/11, of course. The terror organisation moved into Iraq only when bin Laden saw that then US President George W. Bush and Vice President Dick Cheney were getting ready to invade Iraq in 2003. He set a trap. By 2006, al-Qaeda in Iraq had plunged the country into civil war, pitting Shia against Sunni. Only the brave efforts of American Marines and GIs prevented the complete collapse of the state. Now al-Qaeda has come back in Iraq, raising its black flag over territory once fought over so hard by the Americans.

Can the same tragedy be repeated in Afghanistan and Pakistan? The longest war in American history will largely end for Americans this year. But it will not end for Afghans or Pakistanis. Pakistan will continue to be the principal supporter and patron of the Afghan Taliban. Pakistan provides the Taliban with safe haven and sanctuary to train and recruit its fighters, and protects its leaders, including Mullah Omar. The Pakistani intelligence service, the ISI, helps train and fund the Taliban.

For the last few years, the US has also fought a second war from Afghanistan, the counter-terrorist war inside Pakistan. Al-Qaeda found a new base in Pakistan after the rout of Mullah Omar’s Afghan emirate in 2001. The highlight of this second covert war was the Seal raid to kill bin Laden in Abbottabad. Drone missions to disrupt al-Qaeda operations in Pakistan have been more frequent: by one count, there have been 340 lethal missions since President Barack Obama took office and more than two dozen just last year.

Once American forces are gone from Afghanistan, the drone war will be more difficult to prosecute. If Washington reaches an agreement with Afghanistan President Hamid Karzai on signing the bilateral security agreement already negotiated, a residual US counter-terrorism capability can remain in Afghanistan. If there is no bilateral security agreement, it will be much more difficult, if not impossible, to conduct counter-terror missions inside Pakistan. Kabul simply won’t allow it.

Raids like the one on Abbottabad, for example, will be much more difficult to conduct without bases in Afghanistan. Instead of a short flight from a base in Afghanistan, craft will need to be flown from carrier battle groups hundreds of miles away in the Arabian Sea. In all likelihood, the Abbottabad raid would have failed had it been flown from the Arabian Sea, just like the Iranian hostage rescue mission failed in 1980. Too far to fly.

Once American pressure on al-Qaeda in Pakistan subsides, its regeneration will be fast given the huge jihadi infrastructure in Pakistan and the ISI’s incompetence and/ or collusion with the jihadists. Al-Qaeda’s Pakistani allies like the Lashkar-e-Toiba, the Pakistan Taliban and others will gladly help al-Qaeda recover, especially when the danger of a drone strike is much reduced.

Pakistan’s Prime Minister Nawaz Sharif is likely to be even less vigorous in fighting al-Qaeda than Asif Ali Zardari. Zardari did see al-Qaeda as a threat; he knows it helped kill his wife, Benazir Bhutto. During Sharif’s previous two terms in office in the 1990s, the jihadist Frankenstein’s monster in Pakistan blossomed. Despite repeated requests from President Bill Clinton between 1997 and 1999, Sharif took no action to apprehend bin Laden, attack his infrastructure in Pakistan and Afghanistan or to pressure the Taliban and Mullah Omar to control or extradite him to Saudi Arabia. During Sharif’s election campaign in 2013, his party’s rallies and candidates were never attacked by the Taliban or other jihadists, while those of the other parties were under constant fire and attack.

So, al-Qaeda may well recover in months, not years, after American forces depart Afghanistan, if the pressure on its base in Pakistan dwindles. But that is not an argument to stay in Afghanistan with thousands of troops. Obama has done what can be done to help the Afghans defend themselves against the Taliban and al-Qaeda. After seven years of shameful neglect by his predecessor, Afghanistan has got from Obama the support and time needed to build up its own security forces to fight the Taliban without Nato boots on the ground. If the Afghan army cannot handle the Taliban now with important but limited American help, it never will be able to do so.

This is instead an argument for Washington to work with Kabul to keep a limited but robust US counter-terrorist capability in Afghanistan after the drawdown later this year to deal with threats on Afghan territory and from safe havens like Abbottabad across the border for the foreseeable future. Only that will prevent another al-Qaeda renaissance in the most dangerous country in the world, Pakistan.