
Bush came into office with the legitimacy of his Presidency in question by some, following the very close election results and the controversial ruling of the United States Supreme Court to suspend the recount of the Florida results in the election. On September 11, 2011, terrorists attacked the World Trade Center in New York by crashing two airliners into the buildings. A third plane was crashed into the Pentagon in Washington, while a fourth hijacked plane was crashed following the heroic efforts of passengers to avoid further destruction. The incidents were a major turning point in Bush's presidency. That evening, he addressed the nation from the Oval Office, promising a strong response to the attacks. He also emphasized the need for the nation to come together and comfort the families of the victims.
On September 14, he visited the sight of the New York City attacks, known as "Ground Zero", where he met with Mayor Rudy Giuliani, firefighters, police officers, and volunteers. Bush addressed the gathering using a megaphone while standing on a heap of rubble. When someone from the crowd called out to tell Bush that he couldn't hear the President, Bush responded: "I can hear you. The rest of the world hears you. And the people who knocked these buildings down will hear all of us soon."
The attacks were planned and carried out by the terrorist organization Al-Qaeda, led by Osama bin Laden. In a September 20 speech, Bush condemned bin Laden and Al-Qaeda, and issued an ultimatum to the Taliban regime in Afghanistan, where bin Laden was operating, to "hand over the terrorists, or share in their fate".
Bush announced a global War on Terror. The Afghan Taliban regime was not forthcoming with bin Laden, so Bush ordered the invasion of Afghanistan to overthrow the Taliban regime. In his January 29, 2002 State of the Union Address, he told the nation that an "axis of evil" consisting of North Korea, Iran, and Iraq was "arming to threaten the peace of the world." He said that the United States had the right to wage preemptive war, or preventive war.
On October 7, 2001, U.S. and British forces initiated bombing campaigns that was followed by the arrival of troops in Kabul on November 13. The goals of the war were to defeat the Taliban, drive al-Qaeda out of Afghanistan, and capture key al-Qaeda leaders. In December 2001, the Pentagon reported that the Taliban had been defeated, but cautioned that the war would go on to continue weakening Taliban and al-Qaeda leaders. Later that month the UN had installed the Afghan Transitional Administration chaired by Hamid Karzai.
Efforts to kill or capture al-Qaeda leader Osama bin Laden were unsuccessful. He escaped capture in a battle in December 2001 in the mountainous region of Tora Bora, which the Bush Administration later acknowledged to have resulted from a failure to commit enough ground troops. Despite the initial success in driving the Taliban from power in Kabul, by early 2003 the Taliban was regrouping, amassing new funds and recruits. By 2006, the Taliban insurgency appeared larger, fiercer and better organized than expected, with large-scale allied offensives such as Operation Mountain Thrust attaining limited success. As a result, Bush commissioned 3,500 additional troops to the country in March 2007.
Beginning with his January 29, 2002 State of the Union address, Bush began publicly focusing attention on Iraq, expressing concerns that the nation possessed weapons of mass destruction which posed a threat to Americans. In the latter half of 2002, CIA reports asserted that Saddam Hussein was intent of reconstituting his nuclear weapons programs, that he had not properly accounted for Iraqi biological and chemical weapons, and that some Iraqi missiles had a range greater than allowed by the UN sanctions. Critics accused the Bush Administration of manipulating or exaggerating the threat. In late 2002 and early 2003, Bush urged the United Nations to enforce Iraqi disarmament mandates, precipitating a diplomatic crisis. In November 2002, Hans Blix and Mohamed ElBaradei led UN weapons inspectors in Iraq, but were advised by the U.S. to depart the country four days prior to the U.S. invasion, despite their requests for more time to complete their tasks. The U.S. initially sought a UN Security Council resolution authorizing the use of military force but withdrew the request in the face of vigorous opposition from several countries.
More than 20 nations, designated the "coalition of the willing" joined the United States in invading Iraq, with Great Britain being the largest of the other nations. They launched the invasion on March 20, 2003. The Iraqi military was quickly defeated and the capital city of Baghdad fell on April 9, 2003. On May 1, Bush declared the end of major combat operations in Iraq. The initial success of U.S. operations increased his popularity, but the U.S. and allied forces faced a growing insurgency led by sectarian groups, and following a public relations disaster known as Bush's "Mission Accomplished" speech, support for the war decreased. From 2004 until 2007, the situation in Iraq deteriorated further, with some observers claiming that there was a full-scale civil war occurring in Iraq. Bush's policies met with criticism, and his opponents demanded that he set a timetable to withdraw troops from Iraq. The 2006 report of the bipartisan Iraq Study Group, led by James Baker, concluded that the situation in Iraq was "grave and deteriorating". Bush admitted that there were strategic mistakes made in stabilizing Iraq, he maintained he would not change the overall Iraq strategy.
In January 2005, free, democratic elections were held in Iraq for the first time in 50 years. Jalal Talabani was elected as President and Nouri al-Maliki as Prime Minister of Iraq. A referendum to approve a constitution in Iraq was held in October 2005.

On January 10, 2007, Bush announced a surge of 21,500 more troops for Iraq. Three months later, on May 1, 2007, he used only his second veto to reject a bill setting a deadline for the withdrawal of U.S. troops, stating that a continued U.S. presence there was crucial.
By July 2008, American troop deaths had reached their lowest number since the war began, and due to increased stability in Iraq, Bush announced the withdrawal of additional American forces. Bush left office in January of 2009, turning the two wars over to his successor. On May 2, 2011, President Barack Obama called Bush, who was at a restaurant with his wife, to inform him that Osama bin Laden had been killed. The Bushes later joined the Obamas in New York City to mark the tenth anniversary of the September 11, 2001, terrorist attacks. At the Ground Zero memorial, Bush read a letter that President Abraham Lincoln wrote to a widow who lost five sons during the Civil War.