The US invasion of Afghanistan in October 2001 led to the franchising of al-Qaeda. While its top leadership found refuge in Pakistan, the organisation spread its operations into various Middle Eastern countries. For this purpose, Osama bin Laden collaborated with Abu Musab al-Zarqawi, a Jordanian of Palestinian origin, who had visited Afghanistan after establishing the Organisation of Monotheism and Jihad (Jamaʾat al-Tawhid wal-Jihad). In March 2003, the toppling of Saddam Hussein by the US military paved the way for the expansion of al-Zarqawi’s organisation into Iraq. In October 2004, al-Zarqawi pledged allegiance to bin Laden and took over the local branch of al-Qaeda.

However, he did not remain obedient to the central leadership. Despite bin Laden’s objections, al-Zarqawi initiated an anti-Shiʿa campaign that brought the country to the brink of civil war. In June 2006, he was killed in a US air strike and was replaced by Abu Hamza al-Muhajir. The new leader reverted to al-Qaeda’s orbit, but he was killed in a joint US–Iraqi operation in April 2010.

Abu Bakr al-Baghdadi then became the head of the local branch of al-Qaeda, which had changed its name to the Islamic State of Iraq. The rise of al-Baghdadi coincided with the outbreak of the Arab Spring revolutions. While fighting against the Shiʿa-dominated regime in Baghdad, al-Baghdadi decided to expand into Syria sometime in 2011. As a result, the al-Qaeda affiliated Support Front for the People of Syria (Jabhat al-Nusra li Ahl al-Sham) was established in north-western Syria by Abu Mohammed al-Julani. In April 2013, al-Baghdadi attempted to take over the Syrian branch; al-Julani referred the issue to the new leader of al-Qaeda, Ayman al-Zawahiri, who had been chosen after the killing of bin Laden by US forces. While he ruled against the merger of the two branches, al-Baghdadi ignored the mother organisation and attempted to absorb the Syrian branch by establishing the Islamic State of Iraq and Syria (ad-Dawlah al-Islamiyah fi l-Iraq wa-sh-Sham). In June 2014, he declared himself a caliph in Mosul.

Although al-Qaeda and ISIS are two different organisations, they have shared many common features. First, both groups have adhered to the ideology of jihadi-Salafism.