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The Secret Apparatus

Who Is Sisi of Egypt? A Reformer.

Who Is Sisi of Egypt? A Reformer.
16 minute read

Published in the Middle East Quarterly

By Cynthia Farahat

In August 2012, Mohamed Morsi, Egyptian president and leader of the Muslim Brotherhood, appointed general Abdel Fattah as-Sisi, then head of military intelligence, as minister of defense in place of Field Marshal Hussein Tantawi. Given his leadership position in the largely Islamist Egyptian army and his family ties to one of the Brotherhood’s cofounders, Abbas as-Sisi,[1] the new minister of defense was widely expected to promote the Brotherhood’s agenda.[2] Instead, not only was Sisi to engineer the overthrow of the Brotherhood regime in July 2013, but he has turned out to be the most moderate president in Egypt’s modern history, and among the most enlightened of Muslim politicians anywhere.

As a member of the Egyptian military, it was widely expected that Abdel Fattah as-Sisi would further the military’s Islamist views rooted in the philosophy of the Muslim Brotherhood. But his actions to de-radicalize Egypt and reform religious views in Egyptian society have been revolutionary and unprecedented.

The Military’s Muslim Brotherhood Roots

The modern Egyptian military grew from the Muslim Brotherhood’s Special Apparatus (at-Tanzim al-Khass, also known as the Secret Apparatus, at-Tanzim as-Siri), established in 1936 by the Brotherhood’s founder Hassan al-Banna, and the Nazi-allied mufti of Jerusalem, Hajj Amin al-Husseini.[3] During World War II, the Special Apparatus expanded its recruitment of army and police officers, including two future presidents: Gamal Abdel Nasser and Anwar Sadat.[4]

The new recruits operated in a clandestine subdivision called Dubbat al-Ikhwan (the Brotherhood Officers), which functioned under this title until Banna’s assassination in February 1949 and the imprisonment of several Brotherhood officers on terrorism charges. This compelled Nasser to replace the “Brotherhood Officers” with “The Free Officers,” a name untainted by the Brotherhood’s numerous crimes.[5]

The Free Officers later became the perpetrators of the 1952 putsch that toppled the monarchy, but their relations with the Brotherhood quickly soured as Hassan Hudaybi, who succeeded Banna as the organization’s Supreme Guide, would not incorporate the Special Apparatus into the new regime’s security structures, sacking some Free Officers loyalists at its helm, including Nasser’s friend and Special Apparatus head, Abdel Rahman Sanadi.[6]

Matters came to a head in September 1954 when Hudaybi rebuffed Nasser’s demand to dissolve the Special Apparatus and refrain from publicly criticizing his policies.[7] The following month, on October 26, a Brotherhood activist made an attempt on Nasser’s life while he was making a speech in Alexandria. This led to the arrest of thousands of Brotherhood members and the execution of six of its leaders, precipitating a prolonged and bitter fight between the regime and the Brotherhood.[8] In 1965, the regime responded to the uncovering of a fresh assassination plot against Nasser with mass arrests of Brotherhood activists and the execution of more leaders, including the organization’s chief ideologue, Sayyed Qutb.

This power struggle notwithstanding, and despite severing official ties with the Brotherhood, Nasser seemed unable to break completely from the organization and maintained the government positions of some of its leaders and activists, such as Muhammad Ghazali. Appointed to government positions at al-Azhar University in Cairo, an Islamist institution, Ghazali served in both Nasser’s and Hosni Mubarak’s administrations and was responsible for the 1992 fatwa that authorized the killing of Egyptian secular intellectual Farag Fouda.[9] Nasser also appointed convictedBrotherhood terrorist Sayyed Sabe to government and al-Azhar leadership positions, where he served until the early 1990s.[10]

Egyptian presidents (left to right) Gamal Abdel Nasser and Anwar Sadat were, at one time, both members of the Muslim Brotherhood’s Special Apparatus. Also pictured are Egyptian leaders Ali Sabri and Hussein ash-Shafei, Alexandria, 1968.

Under Sadat, the government stopped its repression of the Brotherhood allowing it to become an official parliamentary opposition party. For years, the Brotherhood opposed Sadat for his few free market reforms and for Egypt’s peace treaty with Israel.[11] But the president remained tolerant of the organization until one month before his assassination when he finally responded to a stream of fatwas ordering his death by expressing public regret for releasing Brotherhood operatives from prison and rightfully equating them with the Egyptian al-Gama’a al-Islamiya (GI) terrorists.[12]

Mubarak continued Sadat’s early path of appeasing and empowering the Brotherhood. In a 2011 speech, Brotherhood strategist Khairat ash-Shater stated that the organization had enjoyed “relative freedom” under the Mubarak regime as the president believed that the “Muslim Brotherhood can be part of the political process.”[13]

In 1990, when the Islamic Salvation Front won the majority of votes in the Algerian parliamentary elections, the Egyptian regime started to monitor the Brotherhood more closely, and in 1992, the government discovered that it was still operating the Special Apparatus in Egypt. The investigation was known as the “Salsabil” case, the name of a software company owned by Shater and Brotherhood strategist and financier Hassan Malek.[14] While Mubarak’s regime was suspicious of the Brotherhood, the group still had freedom of assembly and speech as well as much power in many, if not most, government institutions. On the other hand, non-Islamist dissidents were banned and intimated.

Following Mubarak’s overthrow in 2011, new facts about the relationship between the Brotherhood and the Egyptian military leadership came to light. Thus, for example, former Brotherhood leader Tharwat Kherbawy disclosed that the Brotherhood had infiltrated the military[15] while this author uncovered a conspiracy between the Brotherhood and the military leadership to murder Coptic Christians in 2011.[16] Indeed, the military intelligence officer assigned to oversee the purging of officers with Brotherhood or other Islamist affiliations was himself a Brotherhood member, elected in the 2012 parliamentary elections on the group’s Freedom and Justice Party ballot.[17] The military-Brotherhood symbiosis ultimately led to fraudulent presidential elections that installed Morsi in power.[18]

Islamism having been since 1952 the core ideology of the Egyptian military, it was widely expected that Sisi would sustain the Brotherhood’s outlook. In fact, the opposite transpired: Sisi’s actions have been revolutionary and historically unprecedented, both in Egypt and in the history of most Muslim majority countries, especially his attempt to de-radicalize Egypt and reform the religious views he inherited from his predecessors.

Protecting Egypt’s Religious Minorities

Sisi took great pains to protect Egypt’s Christian community, going so far as to undertake military action on their behalf. When ISIS decapitated twenty-one Coptic Christian construction workers in Libya and then aired the horrific video online on February 15, 2015, the Egyptian government retaliated quickly with airstrikes against jihadist targets in Libya, killing sixty-four ISIS terrorists, including three of the group’s leaders. In a fierce and unapologetic message, a presidential spokesman said the attacks were “to avenge the bloodshed and to seek retribution from the killers.”[19] The government also proudly aired the attacks on the jihadists on television.[20]

No less significantly, for the first time since 1952, the Egyptian government enforced capital punishment against Muslims who murdered Christians, executing an Islamist in December 2018 who had slashed the throat of a Christian liquor store owner.[21] Under previous presidents, Muslims who murdered Christians were rarely prosecuted, and capital punishment for murder had never been applied when the perpetrator was Muslim and the victim was Christian. Indeed, under former regimes, the government almost encouraged such attacks by sponsoring “reconciliation sessions” where victims and their families were further intimidated by the government into accepting such injustice while remaining silent.

Egyptian Coptic pope Tawadros II (right) and President Sisi (center) walk together at St. Mark’s Cathedral, Cairo, February 2015. Demonstrating his belief in religious tolerance, Sisi has also attended Christmas mass where he expressed his support for Coptic Christians.

The only time a Muslim was sentenced to death for a terrorist attack against Christians was in 2010 when three Islamists screaming “Allahu Akbar” shot at Christians outside a church in Nag Hammadi, killing six Copts and a Muslim police officer. Two of the alleged perpetrators were acquitted of all charges, and the man who accidently shot the Muslim police officer was sentenced to death and executed in 2011.[22] It is safe to assume that the death sentence was handed down for killing the Muslim police officer rather than the Christians. President Sisi has rectified this grave injustice against Copts.

Sisi is also the first ruler to fund restoration of churches attacked by jihadists. During Morsi’s rule, the Brotherhood attacked seventy-three churches and numerous Christian-owned properties.[23] Sisi’s government restored almost all these churches with the president personally overseeing the project. “This is not a favor; this is your right,” he told Coptic leaders.[24] Sisi’s open defiance of Shari’a law, which relegates non-Muslim subjects to inferior dhimmi status, was further demonstrated by his unprecedented annual attendance at Christmas Mass where he usually gives a short talk to express his support for the Coptic Christians and his commitment to religious tolerance.[25]

In a similar vein, Sisi has been the first modern Egyptian president to renovate Egyptian Jewish heritage sites and synagogues. During the country’s first interfaith celebration of Hanukkah last December, the Egyptian minister of archeology announced that the government would allocate $71 million to the project.[26] This may not come as a surprise given Sisi’s uncompromising message and policies of religious tolerance. But it is bittersweet given Egypt’s belated acknowledgement of its rich Jewish heritage, long after Nasser brutalized and destroyed the country’s Jewish community.

Sisi’s exceptional goodwill vis-à-vis Egypt’s religious minorities can perhaps be encapsulated in his assertion that not only should there be full equality between Egyptian Muslims and Christians but that “we would die for them [i.e., Christians].”[27] As a complete reversal of traditional Muslim attitudes to religious minorities, this assertion constitutes an effective embrace of the modern concept of citizenship. Such an idea does not exist in Islamic ideology and law where the inhabitants of Muslim-majority lands are subject to vastly different laws depending on their religion, gender, sexual orientation, social status, and skin color.

Fighting Islamism in State Institutions

In addition to Sisi’s protection of religious minorities, he has initiated a “de-ikhwanification” (de-Brotherhoodification) of Egyptian state institutions. All of Sisi’s predecessors had played the same game of “tactically empower[ing] Islamists as a foil to gain Western support, arms, and money.”[28] Yet the presence of Brotherhood operatives in the police, military, and bureaucracy is the greatest obstacle to Sisi’s policies and the reforms initiated since his first days in power.[29]In a boost to the president’s reformist line, the Supreme Administrative Court in Cairo has recently endorsed the government’s right to fire individuals affiliated with the Brotherhood.[30]

Also, among Sisi’s most important counterterrorism measures was shutting down 20,000 mosques in Egypt before Ramadan 2018, a rather exceptional move not only in Egypt but in all Muslim-majority nations. Sisi understands how Islamists use mosques to recruit terrorists and radicalize Muslims. Many of these mosques are still sometimes open for prayer during the week, but never for Friday sermons, often used by Islamists to agitate, recruit, and mobilize sympathizers.

Challenging Islamist Precepts and Practices

Sisi is perhaps the first Muslim ruler to criticize the continuous state of jihad, known in Sunni theology as dawam al-jihad (the permanence of jihad). In Sunni eschatology, perpetual jihad only ends when Islamists kill al-masih ad-dajjal (the false messiah).[31] In Shiite eschatology, it is practiced until the earth is cleansed of non-Muslims, and the sun rises from the west.[32]

While Sisi has never used the term dawam al-jihad, he has given a clear message to those who study Islamic theology and are aware of the dangerous concept. During one of his talks about the importance of reformation, the president askedrhetorically,

Is war an exception or is it a constant? War is the exception. When the thought of a nation is exclusively centered on war—at least for the past 100 to 200 years, [and] their understanding of their religion is that war is a constant and peace is an exemption, how is this a religious interpretation?[33]

The permanence of jihad is at the core of Islamism, which Sisi’s critique confronts head-on.

Among Sisi’s bravest positions is his defense of dissenting views upheld by such groups as the Qur’anists (those who consider the Qur’an the only source of divine religious authority and reject the Shari’a).[34] While Qur’anists and those sharing some or all their beliefs are widely persecuted in Egypt and often imprisoned via blasphemy laws, Sisi had no qualms about supporting them ideologically in front of their chief critic, the radical al-Azhar grand imam Ahmad Tayeb, who has admonished those who do not adhere to the Sunna. Sisi’s defense addresses the belief by Sunni fundamentalists that the Sunna (Islamic laws and traditions based on the words and actions of the prophet Muhammad) should be ritualistically and politically observed. These ideas are in opposition to the belief that individual Muslims should be allowed to interpret the Qur’an as they see fit and reject Shari’a law. On these points, Sisi reasoned,

The biggest problem facing the world, and our Islamic world, is not whether or not we follow the Sunna of our Prophet Muhammad, peace be upon him, or whether we don’t follow it. These are just statements that people make. The real problem we face is the wrong interpretation of the basis of our religion. … People who say let’s not adhere to the Sunna of Prophet Muhammad, peace be upon him, and [instead] say let’s only adhere to the Qur’an, are they committing a bigger offense than what we have committed—in terms of our wrong interpretation and extreme radicalism across the world? What is the reputation of Muslims across the world?[35]

Sisi has voiced dissenting views in front of critics, including the radical al-Azhar grand imam Ahmad Tayeb (above). Sisi’s ideas support the belief that individual Muslims should be allowed to interpret the Qur’an as they see fit and reject Shari’a law. He has also defended atheism.

Coming right after Tayeb’s admonition, Sisi’s words unleashed a backlash by Islamist media outlets such as Aljazeera, censuring the president and describing the debate between the two men as a “duel.”[36]

Nor was this the furthest Sisi has gone in defending ideological diversity. In another address to Azhar scholars, he defended the waves of atheism that developed in Egypt as an understandable reaction to the brutality of the Brotherhood’s rule: “People are saying that many young people became atheists. It means they are not apostates from Islam.”[37] This can be confusing to those unfamiliar with peaceful and inclusive interpretations of Islam that categorically reject excommunication—a status associated with a death sentence in both Sunni and Shiite Islam.

According to these moderate interpretations, most notably expressed by the Qur’anists, it is polytheism rather than denial of the existence of God that constitutes apostasy from Islam; and in contrast to Sunnis and Shiites, the Qur’anists do not believe that even these polytheist apostates should be subjected to ritual torture and death.[38]

Sisi continued to justify why people are turning to atheism, saying it was because “they couldn’t tolerate the amount of division, abuse, and injustice they see. They couldn’t take it.” Small wonder that atheist figures in Egypt welcomed this view stating, “President Sisi’s comments about us were positive, and his statements call for peaceful coexistence and tolerance.”[39]

In sharp contrast to previous Egyptian presidents who were infamous for their xenophobia and disparagement of the West, Sisi has shown respect for Western values and sovereignty, telling a Youth World Forum:

If you go to another country as a guest, you must completely abide by its laws, customs, traditions, and culture. If you are not willing to do this, don’t go.[40]

This stance on assimilation in Western societies is highly unorthodox among Muslim-majority governments and is the complete opposite of the Islamist position that views migration as a form of jihad to subvert and ultimately subjugate the West to Shari’a law.

Still, Sisi has been stymied by al-Azhar’s religious leaders in some of his reforms, for instance, amendment of Islamic law to prevent husbands from verbally divorcing their wives[41] and moderating al-Azhar’s curriculum, which teaches that it is religiously permissible to cannibalize, rape, gouge out the eyes, and torture infidels to death.[42]


Sisi is not an Islamist but quite the reverse. Under a constitutional theocracy and in the face of incredible domestic and regional adversity, he has become the most moderate Egyptian president in history. Many of Sisi’s policies and much of his religious discourse are unprecedented and revolutionary, not just in Egypt, but in the history of Islamic rule.

Perhaps Sisi’s most important contribution is his attempt to restore Egypt’s identity, which has been decimated by Islamism under previous presidents while guided by the military and al-Azhar religious authorities. Having inherited a brutal Islamist police state, Sisi could have continued the failed, radical legacy of his predecessors, yet he chose to go the opposite direction. As a result, Egyptian culture is beginning to rediscover the values that had been lost thanks to the 1952 putsch and the Brotherhood’s prolonged influence. Thus, for example, while during Mubarak’s last decade buying a Christmas tree was often a dangerous ordeal, today many Cairo neighborhoods display Christmas trees and
decorations in major squares for the first time in Egypt’s history.[43]

It is, of course, possible to point to the empty half of the glass, notably al-Azhar and government Islamists’ obstruction of some of Sisi’s attempted reforms. Yet, while there is certainly room for improvement in the regime’s governance and policies, it is no less important to recognize President Sisi for the historic reformer he is.

Cynthia Farahat, a Middle East Forum Writing Fellow and columnist for Al-Maqal and Al-Dustur newspapers, is currently working on a book about the Muslim Brotherhood.

[1] El-Watan News (Cairo), Aug. 20, 2012.

[2] See, for example, Daniel Pipes and Cynthia Farahat, “Morsi Could Discredit the Muslim Brotherhood Rule,”, Nov. 14, 2012.

[3] Tharwat Kherbawy, Sir al-Ma’bad (Cairo: Dar Nahdat Misr, 2012), p. 222.

[4] Khaled Mohieddin, Memories of a Revolution (Cairo: American University of Cairo Press, 1995), p. 45; Muhammad Anwar as-Sadat, al-Bahth an az-Zat (Cairo: al-Ahram, 1979), pp. 3-34; al-Araby (London), Aug. 22, 2018.

[5] Muhammad Adawi, “Haqa’iq wa-Asrar,” The Official Muslim Brotherhood Encyclopedia,

[6] Muhammad Hamad Abu-l-Nasr, “Haqiqat al-Khilaf baina al-Ikhwan al-Muslimin wa-Abdel Nasser,” The Official Muslim Brotherhood Encyclopedia,; “Tharwat Kherbawy: Abdel Hakim Amer lahu Dawr fi Kashf Jarimat Muhawalat Ightial Gamal Abdel Nasser,” YouTube, Jan. 22, 2019.

[7] Abu-l-Nasr, “Haqiqat al-Khilaf.”

[8] Al-Masry al-Youm (Cairo), Oct. 26, 2018.

[9] El-Watan News, June 6, 2018.

[10] “Sayyed Sabe,” The Official Muslim Brotherhood Encyclopedia,

[11] El-Youm el-Sabe (Cairo), Dec. 26, 2018.

[12] “As-Sadat Yatahadath an al-Gama’a al-Islamiya wa-l-Ikhwan,” YouTube, May 9, 2012.

[13] “Mashrou an-Nahda al-Islami,” YouTube, Apr. 24, 2011.

[14] “Akhar an-Nahar: Lika Mukhtar Nouh,” YouTube, June 1, 2015.

[15] Kherbawy, Sir al-Ma’bad, p.183.

[16] Jake Sullivan to Hillary Clinton, “H: intel. Secret Offer to El Baradei/Muslim Brotherhood-Army Alliance,” Nov. 23, 2011; Cynthia Farahat, “Clinton Was Aware of SCAF/Brotherhood Conspiracy to Murder Christians in Egypt,”, Nov. 17, 2016.

[17] Al-Arabiya (Dubai), Feb. 2, 2013; Pipes and Farahat, “Morsi Could Discredit Muslim Brotherhood Rule.”

[18] “Mukhtar Nouh: Ana Shahid ala Tazwir Intikhabat ar-Ra’is,” YouTube, Jan. 3, 2018; Daniel Pipes and Cynthia Farahat, “Egypt’s Sham Election,” National Review Online, Dec. 6, 2011.

[19] The Guardian (London), Feb. 17, 2015.

[20] “Al-Muqatalat al-Masriya Taqsef Mawaki Da’esh Libya,” YouTube, Feb. 16, 2015.

[21] Al-Arabiya, Dec. 31, 2018.

[22] Al-Masry al-Youm, Feb. 21, 2011.

[23] Egypt Today (Giza), Aug. 14, 2017; Asia News (Pontifical Institute for Foreign Missions, Vatican), Aug. 17, 2013.

[24] Al-Mogaz (Cairo), Jan. 7, 2018.

[25] Aljazeera TV (Doha), Jan. 7, 2015.

[26] Smadar Perry, “Egypt to renovate its Jewish heritage sites,” YNet News (Tel Aviv), Dec. 12, 2018.

[27] Al-Masry al-Youm, Jan. 19, 2018.

[28] Pipes and Farahat, “Egypt’s Sham Election.”

[29] Al-Arabiya, Nov. 6, 2014.

[30] El-Fagr (Cairo), Oct. 29, 2018.

[31] Abu Dawud Sulayman as-Sijistani, Sunnan Abi Dawud (Beirut: Dar Ibn Hazm, 1997), vol. 3, p. 10.

[32] Muhammad ibn Ya’qub al-Kulayni, Al-Kafi (Tehran: Dar al-Kitab al-Islamiya, 1948), vol. 5, pp. 9-10.

[33] “Al-An: kalimat ar-ra’is khilal fa’iliat al-mu’tamar al-watani as-sadis,” YouTube, July 28, 2018.

[34] Ahmad Mansour, “Birth of the Quranist Trend and Ahmad Subhy Mansour,” Ahl AlQuran, International Quranic Center, Va.

[35] “Kalimat ar-Ra’is khilal ihtifal bi-zikra al-Mawlid an-Nabawi ash-Sharif,” YouTube, Nov. 19, 2018.

[36] Aljazeera, Nov. 20, 2018.

[37] Shorouk News (London), July 16, 2015.

[38] “Dr. Ahmad Subhi Mansour: lah’hazat Qur’ania 401: al-kufr laisa inkar lilah ta’ala,” YouTube, July 12, 2018.

[39] Shorouk News, July 16, 2015.

[40] “Hiwar maftouh baina ar-ra’is as-Sisi wa-a’dad min ash-Shabab,” YouTube, Nov. 4, 2018.

[41] CNN Arabic, Jan. 25, 2016; Egypt Today, Feb. 28, 2018; France 24 TV, Feb. 5, 2017.

[42] Cynthia Farahat, “Is Al-Azhar University a Global Security Threat?” American Thinker, Aug. 23, 2017; CNN Arabic, Sept. 22, 2014.

[43] Al-Ahram (Cairo), Dec. 12, 2018.