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Beginning with their invasion of Afghanistan and toppling of the al Qaeda-harboring Taliban government in 2001, the U. S. and its allies have been engaged in protracted military conflicts and peacekeeping operations in Afghanistan and elsewhere. A United States-led coalition bombed and invaded the sovereign nation of Iraq in 2003, toppling the government of President Saddam Hussein.

Due to continuing insurgencies against coalition occupying forces and against the coalition-supported democratic Iraqi government, Iraq has come to be seen by the Bush Administration as "the main front in the War on Terror". Militant Islamic "terrorist" groups have taken advantage of this as a tool for recruitment throughout the Muslim world; for example, Iraqi insurgent leader Abu Musab Al Zarqawi renamed his local "terrorist" group Al Qaeda in Iraq, receiving the blessing of Al Qaeda leaders.

Bush's frequent linking of the Iraq War to the "War on Terror" following the events of 9/11 has been highly controversial both within and outside the United States; proposed links between Iraq and terrorist groups were found to be fabrications, and the invasion of Iraq was widely opposed internationally, although the War on Terror had initially met with more support, at least outside Islamic countries. In early 2002, the U. S.

began transporting prisoners of the Afghan and Pakistani fronts in the War on Terror to an internment camp at its naval base in Guantanamo Bay, Cuba. America officially designated these prisoners as "enemy combatants" who were outside the protections of the Geneva Conventions to which it was a signatory, meeting with near-unanimous international opposition for this policy. The detainees' treatment and lack of defined legal status at Guantanamo has also been under question, including by the U. S.

Supreme Court, which decided against the administration in a landmark ruling. Possibly as a result of such controversies, polls of international public opinion have found that support for the United States since the War on Terror began is at its lowest level in history. Although the U. S. government continues to co-operate in the campaign with governments around the world, such as in Europe, South Korea and the Philippines, the war is no longer widely supported by populations outside the United States and Israel.

The War on Terror also includes moves to halt money flows to US-identified terrorist organizations, and a diplomatic push to convince other nations to do the same. These moves are controversial as well, due to debates over which groups are "terrorist". Islamic groups and charities, and individuals that support them, have often been targeted; many deny terrorist affiliations, and many perceive the War on Terror as a "Clash of Civilizations" or as a "crusade" against Islam (Bush often emphasizes the war is not religiously motivated, but once used the term "crusade" to describe it).

In 2006, the U. S. withdrew its financial aid to the Palestinian Authority when Hamas, which it designated a terrorist group, won democratic parliamentary elections and assumed control. The war has also been perceived by some as an attempt by the U. S. government to "reform" several political regimes in certain countries to make them free market democracies friendly toward the U. S. , a view which the Bush Administration appeared to endorse in its 2005 "freedom" agenda for the Middle East. This view, however, is open to contention.

The war has met with criticism even from some supporters of its general aims, who claim the rhetoric is too broad and too influenced by "neo-conservative" ideas to remake the Middle East in a certain image, and that the war needs to be defined more narrowly in the interest of its participant countries (perhaps specifically around Islamist terrorism against the United States) so as to be "winnable". The U. S. and its allies have claimed several victories in the war on terror, such as the capture of alleged 9/11 planner and Al-Qaeda member Khaled Sheikh Mohammed.

However, American politicians talk about the war in similar terms to the Cold War, treating it as an inevitability that will likely continue for the forseeable future, and which will continue to strongly define the nation's military and political commitments and alliances. In 2002, President Bush designated Iraq, Iran and North Korea an "axis of evil"; there is speculation the War on Terror might expand to include Iran, or Syria. In speeches, Bush has said the war will go on until the goal of "ending international terrorism" has been fully achieved.