Paul Vallely: Wounded al-Qa'ida will lash out more

Weakened by the death of Bin Laden, whose successor is a ruthless killer, the organisation is newly fired up by grievances

If you want to see why torture doesn't work, you need look no further than Ayman al-Zawahiri who was regularly beaten in the jails of the US-backed regime in Egypt two decades ago. There, he claimed, he and his fellow prisoners were kicked, hit, hung over doors, whipped with cables, given electric shocks and had wild dogs loosed upon them. Zawahiri was a dedicated Islamist when he went into jail. By the time he came out he had been hardened into the fanatical and violent terrorist who has just succeeded Osama bin Laden as head of al-Qa'ida.

That was not the only triumph of the torturers. Using techniques which led Zawahiri to say to a fellow prisoner "the death penalty is more merciful than torture", they beat out of him information about a comrade who was then also arrested. Zawahiri felt so humiliated by being made to "destroy his movement with his own hands" and "offer colleagues' secrets to the enemy" that, guilt-ridden, he fled the country determined to avenge the betrayal that had been forced upon him. He moved to Saudi Arabia. There he met Bin Laden.

The differences between the two men offer clues on how global terrorism is may now develop. Both came from privileged backgrounds, but where the Bin Ladens were extremely wealthy from their $5bn construction business, allowing Osama bin Laden to bring vast sums of money to the al-Qa'ida cause, the Zawahiri family was known for a combination of medicine and religious scholarship.

Though Ayman al-Zawahiri grew up in a cosmopolitan part of Egypt he became deeply religious – so much so that the centre of his forehead bears a darkened callus formed by his many hours of prayerful prostration. He trained as an eye surgeon. He did not stay in Saudi long, but travelled to the northern border regions of Pakistan to work in a Red Crescent hospital treating Afghan refugees, driven from their home by the a Soviet army of occupation.

But while the Russians were the enemy, the Egyptian doctor returned to Saudi bristling with the conviction that the Americans, who were arming the Afghan mujahideen, would prove the long-term foe because of their arrogant ideology and economic dominance. Democracy, he concluded, was a form of "polytheism".

The grievances of Bin Laden, by contrast, were much more direct. When the two men met, Bin Laden, then 28, had lived a life of untrammelled wealth and pleasure, with a personal fortune of about £250m. But he had been radicalised by the suffering of Afghan Muslims and had raised hundreds of millions of dollars for the mujahideen resistance. He was concerned at the plight of the Palestinians and outraged that Saudi Arabia – home of Islam's two holiest places – was being defiled by the presence of infidel troops in US bases.

The two men did not at first see eye to eye. Zawahiri's Islamic Jihad movement in 1995 attacked the Egyptian embassy in Pakistan, a move that Bin Laden feared would jeopardise the supply route into Afghanistan. Two years later, Zawahiri organised a mass attack on one of ancient Egypt's most high-profile sites at Luxor, in which 58 tourists were machine-gunned and hacked to death. Such was the international outrage most Islamists tried to disown it.

But by 1998, the two men had formed a loose alliance under the "World Islamic Front Against Jews and Crusaders" umbrella, issuing a fatwa, written by Zawahiri, that ordered all Muslims to kill all Americans and their allies, civilian and military. Bin Laden had the money, but lacked the unifying theological vision. Zawahiri had that, along with a team of doctors, engineers and soldiers who were experienced covert revolutionaries. He brought to Bin Laden the notion that secular, pro-Western Arab governments were as much the enemy as the Soviets, Americans or Israelis. In 2001, the two men's organisations merged into a single entity, Qaeda al-Jihad.

Zawahiri was the organisational brain. He is believed to have been behind the 1993 assault on US troops in Somalia; the 1995 assassination attempt on Egypt's Hosni Mubarak; the 1998 bombings of the American embassies in East Africa; the 2000 attack on a US naval ship in Aden harbour; and the 9/11 attacks in New York and Washington in 2001.

He pioneered the use of suicide bombers, a strategy that necessitated circumventing powerful Islamic prohibitions on suicide and the murder of innocents. He came up with the idea of bombers making videotapes on the eve of their "martyrdom". It was he who began testing biological and chemical weapons; samples of anthrax were found in his house in Afghanistan. He paid Chechen mobsters millions of dollars in cash and heroin in an attempt to obtain radiological "suitcase" bombs left over from Soviet days. In the 1990s, he travelled tirelessly through the Balkans, Austria, the former Russian republics, Yemen, Iraq, Iran, Argentina and the Philippines establishing cells and setting up training camps.

Bin Laden funded all this. But fractures began to appear in al-Qa'ida. In 2005, Zawahiri issued a reprimand to the Sunni head of al-Qa'ida in Iraq for killing too many Shia Muslims and damaging the organisation's reputation in the "race for the hearts and minds" of Muslims worldwide. In 2007, when the group's military commander was killed, Zawahiri and Bin Laden quarrelled over who should succeed him. Revealingly, Zawahiri won, but Bin Laden was not happy.

In the past few years, the relationship between the al-Qa'ida leader and his deputy appears to have been strained. The CIA peddled the line that Zawahiri was the operational and strategic commander, Osama bin Laden only a figurehead. But the computers found in Bin Laden's compound show that he remained deeply involved in planning. Yet there were no clues as to the whereabouts of Zawahiri. One Saudi newspaper has even claimed that Zawahiri convinced Bin Laden to move from his mountain hideout – and then leaked his whereabouts to US intelligence.

What is clear is that relations between the al-Qa'ida organisations in Afghanistan, Yemen, Iraq, Somalia and Algeria are more fragmented than before, with significant disagreements on priorities. The notion that the network can be controlled by a single leader on a day-to-day basis seems implausible. It may explain why it has taken six weeks for al-Qa'ida to announce its new leader.

All this makes al-Qa'ida look weaker but less predictable. Zawahiri may now launch a spectacular attack on the West to avenge Bin Laden's death assert his own credibility. He may revert to his old preoccupation, Egypt, particularly in the light of the Arab Spring to which he is anxious to stake a claim. He may want to focus on Yemen and Somalia which he sees as training grounds for the militants who will bring revolution to Bahrain or Saudi Arabia. Or he may want to foment further discontent in Pakistan, where he has urged the people to rise up against their leaders. Al-Qa'ida may be weaker, but that might well make it even more dangerous.