The first pillar of the Administration argument for ousting Saddam Hussein—its continued active development of WMD—has been researched extensively. The second pillar of the Administration argument—that Saddam Hussein's regime had links to Al Qaeda—is relevant not only to assess justification for the invasion decision but also because an Al Qaeda affiliate (Al Qaeda in Iraq, or AQ-I) became a key component of the post-Saddam insurgency among Sunni Arabs in Iraq. The Administration argument for an Iraq-Al Qaeda linkage had a few major themes: (1) that there were contacts between Iraqi intelligence and Al Qaeda in Sudan, Afghanistan, and Pakistan dating from the early 1990s, including Iraq's assistance to Al Qaeda in deployment of chemical weapons; (2) that an Islamist faction called Ansar al-Islam (The Partisans of Islam) in northern Iraq, had ties to Iraq's regime; and (3) that Iraq might have been involved in the September 11, 2001 plot itself. Some CIA experts reportedly asserted that the ideological differences between Iraq and Al Qaeda were too large to be bridged permanently. However, some accounts question the extent of links, if any, between Baghdad and Ansar al-Islam. Al Qaeda and the Iraq Insurgency

Whether or not Al Qaeda leaders and Saddam Hussein had a relationship, a major issue facing the United States is the degree to which Al Qaeda elements are threatening the U.S. effort to stabilize post-Saddam Iraq. The U.S. troop surge was intended to try to take advantage of a growing rift within the broad insurgency that was being observed by U.S. commanders in Iraq as early as mid-2005. In August 2006, U.S. commanders began to receive overtures from Iraqi Sunni tribal and other community leaders in Anbar Province to cooperate with U.S. efforts to expel AQ-I and secure the cities and towns of the province. This became known as the "Awakening" (As Sahawa). In Baghdad, the U.S. military established supported this trend in the course of the Baghdad Security Plan ("troop surge") by establishing about 100 combat outposts, including 33 "Joint Security Stations" in partnership with the ISF, to clear neighborhoods of AQ-I and to encourage the population to come forward with information about AQ-I hideouts. In late July 2008, a reputed AQ-I leader in Anbar told the Washington Post that AQ-I leader Abu Ayyub al-Masri had left Iraq to go to Afghanistan, or to the border areas of Pakistan where Al Qaeda leaders are believed to be hiding. He testified that AQ-I is "still capable of lethal attacks" and that the United States must "maintain relentless pressure on the organization, on the networks outside Iraq that support it, and on the resource flows that sustain it." This estimate is somewhat higher than what many experts might expect in light of the official U.S. command assessments of the weakening of AQ-I by U.S. operations and strategy. Linkages to Al Qaeda Central Leadership

If the reports of significant AQ-I relocations to the Pakistan tribal areas bordering Afghanistan are correct, this would suggest that the links are tightening between AQ-I and Al Qaeda's central leadership as represented by Osama bin Laden and Ayman al-Zawahiri.
In explaining the decision to invade Iraq and oust Saddam Hussein from power, the Administration asserted, among other justifications, that the regime of Saddam Hussein had a working relationship with the Al Qaeda organization. The Administration assessed that the relationship dated to the early 1990s, and was based on a common interest in confronting the United States. The Administration assertions were derived from U.S. intelligence showing a pattern of contacts with Al Qaeda when its key founder, Osama bin Laden, was based in Sudan in the early to mid-1990s and continuing after he relocated to Afghanistan in 1996.
Critics maintain that subsequent research demonstrates that the relationship, if it existed, was not "operational," and that no hard data has come to light indicating the two entities conducted any joint terrorist attacks. Some major hallmarks of an operational relationship were absent, and several experts outside and within the U.S. government believe that contacts between Iraq and Al Qaeda were sporadic, unclear, or subject to alternate explanations.
Another pillar of the Administration argument, which has applications for the current U.S. effort to stabilize Iraq, rested on reports of contacts between Baghdad and an Islamist Al Qaeda affiliate group, called Ansar al-Islam, based in northern Iraq in the late 1990s. Although the connections between Ansar al-Islam and Saddam Hussein's regime were subject to debate, the organization evolved into what is now known as Al Qaeda in Iraq (AQ-I). AQ-I has been a numerically small but operationally major component of the Sunni Arab-led insurgency that frustrated U.S. efforts to stabilize Iraq. Since mid-2007, in part facilitated by combat conducted by additional U.S. forces sent to Iraq as part of a "troop surge," the U.S. military has exploited differences between AQ-I and Iraqi Sunni political, tribal, and insurgent leaders to virtually expel AQ-I from many of its sanctuaries particularly in Baghdad and in Anbar Province. U.S. officials assess AQ-I to be weakened almost to the point of outright defeat in Iraq, although they say it remains lethal and has the potential to revive in Iraq. Attacks continue, primarily in north-central Iraq, that bear the hallmarks of AQ-I tactics, and U.S. and Iraqi forces continue to conduct offensives targeting suspected AQ-I leaders and hideouts.
As of mid-2008, there are indications that AQ-I leaders are relocating from Iraq to join Al Qaeda leaders believed to be in remote areas of Pakistan, near the Afghanistan border. That perception, if accurate, could suggest that AQ-I now perceives Afghanistan as more fertile ground than is Iraq to attack U.S. forces. The relocation of AQ-I leaders to Pakistan could also accelerate the perceived strengthening of the central Al Qaeda organization.
This report will be updated as warranted by developments. See also: CRS Report RL31339, Iraq: Post-Saddam Governance and Security, by [author name scrubbed].