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The Muslim Brotherhood, or al-Ikhwan (the Brothers) is a Middle Eastern religious and political movement whose stated goal is to instil the Qur'an and Sunnah as the "sole reference point for ordering the life of the Muslim family, individual, community, and state." Unlike Salafis, the movement officially supports the use of democracy and scorns the use of violence to achieve its means, although that doesn't mean all members follow suit; it has, in the past, been home to a militant wing known as the "Special Apparatus." The Muslim Brotherhood has been declared a terrorist organization by Egypt and Russia.
As a result of the first post-revolution elections, the Brotherhood was the chief party in the Egyptian government. However, they took far too long to draft a new constitution, and the people once again took to the streets, inspiring the military to remove the Brotherhood via a coup.
The Muslim Brotherhood was founded in Egypt in 1928 after the collapse of the Ottoman Empire and the subsequent ban of the caliphate system of government that had united the Muslims for hundreds of years. It soon spread throughout the former colonial empires. It was founded on the idea that Islam was not only a religious observance, but a comprehensive way of life, on the tenets of Wahhabism, and substituted the traditional Islamic education for society's male students with jihadi training.
Members of the brotherhood were responsible for the assassination of Egyptian Prime Minister Mahmud Fahmi Nokrash in 1948, an attempt on the life of Egyptian President Gamal Abdel Nasser in 1954, and the murder of Egyptian President Anwar al Sadat in 1981.
Sayyid Qutb, a radical author, espoused overthrowing the secular and Westernized regimes throughout the Islamic world by violent jihad. Qutb was executed by hanging in 1966 for his role in plotting to overthrow Nassar. The Brotherhood began moderating their views and public statements in the 1990s; Ayman al-Zawahiri lashed out against it in his 1991 book The Bitter Harvest (1991) and forged an alliance of his jihadis[note 1] with Osama bin Laden and the al Qaeda organization.
The Muslim Brotherhood remained illegal until the transition of power following the Egyptian revolution of 2011. Muhammad Morsi, the Brotherhood candidate, assumed the presidency and soon openly discussed terminating the peace treaty with Israel and American aid. For the next year a flood of weapons poured into Gaza via the Rafah border crossing with Egypt. Morsi was deposed in mid-2013 and the arms smuggling stopped.
The Syrian Islamic Brotherhood had existed since about 1937. It was banned from participating in political life by Syrian President Adib Shishakli in the early 1950s (MB then was known as the Islamic Socialist Front). Not until the seizure of power by the secular Ba'ath party in 1963 did it form into an opposition group. In February 1964 the Brotherhood instigated riots against Ba'ath party rule in the Islamist stronghold of Hama which were suppressed by the army.
Inspired by the Islamic Revolution in Iran the Brotherhood developed a plan to trigger a similar popular revolt to oust Ba'athist dictator Hafez al-Assad (father of Bashar al-Assad). Beginning in 1979 the Brotherhood forged links with Syrian Ba'athist dissidents and the Iraqi Ba'athist President Saddam Hussein for help in overthrowing Assad. The Iraqi regime provided covert assistance to the Brotherhood rebels in Aleppo, Damascus, and Hama. Saddam Hussein's government accused the Assad regime of human rights violations against the Muslim Brotherhood. According to Wikipedia, after the uprising was brutally crushed in the 1982 Hama Massacre one faction "for several years retained a military structure in Iraq, with backing from the [Iraqi] government."
The Muslim Brotherhood was later vilified by the Salafi theorist Abu Musab al-Suri in his 1991 treatise, Notes on the Jihadi experience in Syria. Among the Brotherhood's "crimes" was its "alliance with parties of infidelity, freethinking (zandaqa), and apostasy".
In June 1980, the Brotherhood attempted to assassinate President Assad following which the government passed a law making membership of the Brotherhood a capital offence; the law is still in force today.
The Jordanian Islamic Brotherhood was established in 1954 with King Hussein's blessing.
In September 1970, the Jordanian army expelled the Palestinian organizations who took refuge in camps in Amman and other Jordanian cities after the Six Day War. The Muslim Brotherhood, which supported King Hussein in his war on the Palestinian organizations, was rewarded with the Jordanian education ministry. The ministry adopted the ideas of Sayyid Qutb and the Salafi-jihadists in shaping the subsequent generations educated with Qutbi curricula supervised by the Muslim Brotherhood.
In 1989, 22 members of the Muslim Brotherhood movement were elected as members of parliament. They also had five cabinet members in the 1991 government. In 1992, after the issuance of the law of parties, the Muslim Brotherhood established a party called the Islamic Labour Front. The Brotherhood refrained from participating in the 1997 elections to protest the government’s signing a peace treaty with Israel in 1994.
Following the crackdown by Abdel Nassar and the hanging execution of Sayyid Qutb, many Egyptian Ikhwan (Brothers) found their way to Saudi Arabia and were initially welcomed by the oldtime scholarly purists who supported the regime of the House of Saud. Qutb's writings were based largely upon the ancient imams, Ibn Taymiyyah and Abd al-Wahhab, founder of the Wahhabi purist movement. The politicized teachings of Qutb gained a foothold among the younger generation.
By the Gulf War of 1991 however, unity began to fray when senior purists issued fatwas in support of the Saudi king which allowed basing U.S. troops in Saudi Arabia in preparation for the liberation of Kuwait. This sent shockwaves through various Islamist organizations. The Salafi movement gained at the expense of the more secularized and rationalist Muslim Brotherhood, and the more parochial supporters of the Wahhabi regime.
American Infiltration Conspiracy Theory
In 2004, a 16-page document known as the Explanatory Memorandum was found in a home in Virginia during an investigation into the Holy Land Foundation, an American Muslim charitable organization that was suspected of funnelling money to Hamas. The document, written in 1991 by Mohammed Akram Adlouni, who might be a Brotherhood official , expresses a desire "destroy Western civilization from the inside" and ensure that Islam is "victorious above all other religions". The bulk of the Memorandum gives steps in order to achieve dominance in the United States. These steps mostly consist of establishing Islamic institutions of various kinds, such as magazines, advocacy groups, and a political party.
The Memorandum's more inflammatory sections have been seized upon by confirmed Islamophobes like Frank "Everyone I don't like is affiliated with the Muslim Brotherhood" Gaffney and Brigitte Gabriel  as proof of a grand conspiracy by the Brotherhood to infiltrate the United States and subvert its government and culture. Some also claim, with no corroborating evidence, that a list of American Muslim organizations in the document proves that these organizations are fronts for the Brotherhood.  Evangelical preacher Franklin Graham claimed Barack Obama aided the Muslim Brotherhood in infiltrating American institutions, saying "The Muslim Brotherhood is very strong and active here in our country. We have these people advising our military and State Department."
The Memorandum has received pretty much no attention outside of wingnut circles, except to point out that the people making a big deal out of it have long track records of bias, how little it actually proves, its highly tenuous connection to the Brotherhood, and its apparently near-total lack of importance to anyone outside its own author. , , 
- The group included Mohammed Islambouli, brother of Sadat assassin triggerman Khaled Islamboul.
- Egypt's Muslim Brotherhood declared 'terrorist group'. BBC News. 2013 December 25.
- Muslim Brotherhood Topics page at the New York Times.
- Muslim Brotherhood, Foreign Intelligence Resource Program, Federation of American Scientists.
- Egypt unrest: Obama increases pressure on Mubarak, BBC, 5 February 2011.
- Jihadi After Action Report: Syria, by Stephen Ulph, William McCants editor. The Combating Terrorism Center, United States Military Academy, West Point, p.6.
- See the Wikipedia article on Salafi jihadism.
- Anatomy of the Salafi Movement, Quintan Wiktorowitcz, Talylor Francis Group, Studies in Conflict & Terrorism, 29:207–239, 2006. PDF pp. 15-19.
- Franklin Graham: World’s Christians in Grave Danger, NewsMax, 18 Mar 2011