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Ever since early April when he became an official candidate in the first post-revolution presidential election, Dr. Mohammad Morsi has been generally dismissed by most political observers as a weak and unimpressive politician. In fact, he was an accidental contender since he was the stand-in candidate for the Muslim Brotherhood’s (MB) first choice, senior leader Khairat Al-Shater. The MB fielded Morsi as its back-up candidate on the last day of filing because it predicted correctly that its original candidate would be disqualified by the pro-SCAF Supreme Constitutional Court (SCC).

As Egypt’s Supreme Council of the Armed Forces (SCAF) took the reigns of power in February 2011, many observers believed that a tacit understanding existed between the powerful Egyptian military and the MB, the most organized political and social group in Egypt. For the next eighteen months, this complicated and largely behind the scenes contentious relationship between these two powerful entities had its ups and downs.

When SCAF sided with millions of Egyptians in ousting Hosni Mubarak in early Feb. 2011, it was not to advance the objectives of the revolution but rather to sacrifice the president in order to save his regime. Throughout 2011, there were three centers of powers in the country: SCAF with its apparent military power, the MB with its enormous capacity for organization and mass mobilization, and the other revolutionary and grassroots groups (dominated by the youth but politically unorganized and inexperienced) taking to the streets throughout the year while paying a terrible price with dozens martyred, hundreds wounded, and thousands detained in military show trials.

When SCAF cracked down on the revolutionary groups, especially during the fall of 2011, the MB refrained from challenging the military as it was in the midst of its campaign for the parliamentary elections. By January 2012, it was clear that the Islamist groups led by the MB had won almost seventy five percent of the seats in both parliamentary chambers. As the MB flexed its muscle and asked to be allowed to form the next government, SCAF refused and threatened the group with the dissolution of parliament. Shortly after, the MB reversed its public promise not to field a contender and actually filed for two presidential candidates.

Within days the military revealed its preferred candidate, Gen. Ahmad Shafiq, the last prime minister of the Mubarak regime. Consequently the tension of the two groups came to the fore as SCAF and the Egyptian deep state (where the remnants of the Mubarak regime still occupied strategic positions and were in control of the state bureaucracy) did everything in their power during the first round of the presidential elections in late May to split the opposition and support their candidate in order to get him to the second round.

Despite their apprehension over the MB’s past broken promises, the revolutionary groups largely coalesced behind Morsi, the other winner of the first round, in the runoff elections, which he barely won with just over 51 percent of the vote. When it became clear on the last day of the runoff elections on June 17 that its candidate might lose, SCAF carried out a sweeping power grab as it dissolved the MB-dominated parliament, reclaimed all legislative powers to itself, issued a constitutional declaration that largely diminished the office of president, and assigned itself the right to appoint the constitution-writing committee if the current one was invalidated as expected by the SCC. In short, by the time Morsi took the oath of office on June 30, SCAF -which essentially ruled the country for the past 16 months- was effectively in control of the most important levers of power relegating the elected president to the position of a figurehead with diminished authority.

By the end of the first week of his presidency, Morsi issued a presidential proclamation, which re-instituted the parliament while calling for new parliamentary elections shortly after the constitution is approved by the people in a national referendum. Within 48 hours, the SCC swiftly overruled him and reversed his decision while affirming SCAF’s constitutional declaration. Morsi reluctantly accepted its decision averting an impending confrontation, which confirmed in the minds of his detractors his weakness and political naiveté.

Morsi’s tactical retreat of this early challenge to SCAF’s power emboldened the remnants of the Mubarak regime as a public campaign of belittling and undermining the newly elected Islamist president began in earnest. Barely a month into his presidency, his opponents, which included not only SCAF and Shafiq supporters, but also anti-Islamic liberal and secular groups, called for mass protests to oust him that were scheduled for August 24 under the theme “toppling the rule of the Brotherhood.”

Meanwhile, Morsi had difficulties forming a government as he faced many obstacles since most political groups and prominent figures tried to impose unacceptable demands that restricted his presidential authority. By the end of July, he opted for a cabinet that was dominated by technocrats. Out of thirty-five cabinet positions, only ten ministers represented pro-revolution figures, five of which were from his own MB-affiliated Freedom and Justice Party (FJP). However, these cabinet ministers occupied some of the strategic positions in government that he hoped would bring about long-term structural reforms including the ministries of Housing, Labor, Information, Education, and Youth. But perhaps the most significant appointment was that of Judge Ahmad Makki as the new justice minister. Makki was well known as one of the fiercest critics of Mubarak and is a long time champion of judicial independence. Upon assuming office he immediately took steps to institute new policies geared towards this goal.

But many other ministers were also carry-overs from previous cabinets including the relatively unknown minister of water resources, Dr. Hisham Qandil, 50, who was elevated to the position of prime minister. Although considered by many as a lightweight, the relatively young American-educated prime minister is well regarded for his efficiency and honesty. Morsi also retained SCAF’s head, Field Marshal Hussein Tantawi as defense minister and the ministers of foreign affairs and finance, as well as the heads of intelligence and other senior military and security leaders. Most observers concluded that Tantawi, SCAF, and the security agencies had won this round and would be in effective control of the most important strategic positions in government.

For the first month of his presidency, Morsi treated the military institutions and SCAF leaders not only with extraordinary respect but even with reverence as he sought to earn their trust. Many assumed that he had accepted SCAF’s constitutional proclamation that relegated him to a secondary role. Many foreign dignitaries visiting Egypt, including Secretary of State Hillary Clinton, made a point in meeting not only with Morsi but also with Tantawi. While in the country even her brief statements were awkward as she counseled the president and SCAF’s head to work together as though the country had two functioning heads of state.

But what everyone failed to see was that during this period Morsi was studying the power relationships within SCAF and the other security agencies. He was able during this brief period to identify those military and security leaders whose loyalty were to Tantawi and his chief-of-staff Gen. Sami Anan. In short, he was waiting for the right moment to make his move with minimal confrontation. Luckily for him that opportunity came soon enough.

On August 5, in the midst of the holy month of Ramadan, dozens of unidentified militants with unclear motives and without any provocation attacked a checkpoint in the Sinai at the Egypt-Gaza border as the unsuspecting soldiers were breaking their fast, killing sixteen guards and wounding seven. As a result, the nation was shocked and enraged. Many political analysts and commentators blamed the lack of security on the military that neglected its main duties in protecting and securing the borders while its leaders were fully engaged in politics and ruling the country despite electing a civilian president.

Morsi immediately seized the moment and visited the Sinai twice in a week declaring his resolve to restore security and punish the perpetrators. However, his critics also took advantage of the tragic attack calling him weak and ineffective. On August 7 Morsi cancelled his appearance to attend the funerals of the fallen soldiers as it came to his attention that he would physically be attacked by the remnants of the Mubarak regime. In fact, many public figures considered by the remnants to be Morsi’s supporters including Qandil, his prime minister, and former presidential candidate Dr. Abdelmoneim Aboul Fotouh, were attacked and insulted during the funeral procession, while SCAF’s leaders and other former Mubarak-regime figures were hailed.

The following day on Aug. 8, Morsi seized the opportunity and dismissed intelligence chief Murad Mowafi, who was Omar Suleiman’s replacement when Mubarak appointed the latter as his vice president in Jan. 2011, during the height of the popular protests. He also sacked two SCAF members (the heads of the military police and the Cairo security force) and replaced them with officials he trusted. Under intense public pressure Tantawi and SCAF could not object although such decisions were technically within their prerogatives as the June 17 constitutional proclamation barred the president from appointing or dismissing any military personnel or ranked officers.

On the morning of Aug. 12, Morsi quietly called the head of military intelligence Lt. Gen. Abdelfattah El-Sisi, 57, and the head of the third army Lt. Gen. Sedky Sobhi, 55, both current SCAF members who behind the scenes have been critical of Tantawi, 76, and Anan, 74, for neglecting the military and delving into politics. Morsi not only promoted them as generals but also offered them the positions of minister of defense and chief of staff, respectively. Upon accepting their new assignments, they were sworn in before the president, his prime minister, and other presidential advisors.

Morsi then called Tantawi and Anan for a meeting that afternoon. Calmly, he thanked them for their service and informed them that they have been dismissed and that their replacements have been sworn in. He also called the military general in charge of military budget Lt. Gen. Mohammad Nasr. After assuring him that he was not dismissed, Morsi ordered Gen. Nasr to report the details of the financial situation at the defense ministry as if to signal the start of a new era in front of Tantawi and Anan.

Morsi also soothed any ill-feeling by the generals as he sent an unmistakable signal to Egypt’s de facto military leaders during the transitional period that they would not be tried or humiliated as he informed them that he would be honoring them in public by presenting them the Collar of the Nile and the Republic, the highest medals in the country. He also appointed them as presidential advisors. Nevertheless, both were reportedly stunned. On his way out of the presidential palace, Tantawi was heard cursing in anger.

Immediately, Morsi’s spokesman, Yasir Ali announced in a nationally televised press conference that the president cancelled SCAF’s June 17 constitutional declaration that assigned many presidential and legislative powers to SCAF. He also announced a new constitutional declaration that transferred the same powers that SCAF allocated to itself in its previous declaration back to the president, including legislative powers in the absence of parliament and the appointment and dismissal of military officers.

During the press conference, Ali also announced the appointment of a new vice president, Judge Mahmoud Makki, the younger brother of the justice minister. The younger Makki also has an outstanding reputation as an exemplary, independent, and powerful jurist. His appointment was seen as a counterweight to any rumblings by the pro-SCAF Supreme Court’s senior justices who might challenge Morsi’s decisions.

Morsi’s spokesman then announced to the nation the dismissal of not only Tantawi and Anan but also the heads of the Navy, Air Force, and Air Defense, the most senior SCAF generals. Understanding the politics within SCAF, all three generals were also reassigned to senior civilian positions as heads of companies running the Suez Canal and military industry productions. State television then aired the images taken that morning of Morsi swearing-in the new defense minister and chief of staff.

Underestimated by his critics and dismissed by his opponents, Morsi has demonstrated coolness under pressure, toughness, and shrewdness uncharacteristic to Egyptian politicians. With the exceptions of Mubarak’s remnants his actions were overwhelmingly approved by Egyptians from diverse political, ideological, and pro-revolution groups.

The new generals Morsi choose to lead the Egyptian military, Sisi and Sobhi, embody a new brand of officers. In their mid-fifties, they represent a new generation distinguished from the Mubarak-era generation in their late seventies. The new defense minister is considered not only a critic of Mubarak and his regime but also of the former senior SCAF leaders. He is also distinguished as a religious person in one of the most secular institutions in the country. This characteristic no doubt has endeared him to the Islamist president. Gen. Sisi is also on record advocating the return of the military to its professional duties and staying away from any engagement in domestic politics. Unlike his predecessors, Gen. Sisi had also publicly criticized NATO’s recent involvement in Libya, and has called for the assertion of Egypt’s sovereignty and independence.

Furthermore, on Aug. 16 the New York Times revealed that the new chief-of-staff, Gen. Sobhi, wrote a paper for the Naval War College seven year ago that was highly critical of American foreign policy in the Middle East, especially with regard to the Palestinian-Israeli conflict. Extraordinarily, he wrote that, “the permanent withdrawal of United States military forces from the Middle East and the Gulf should be a goal of U.S. strategy in the region.”

Taking advantage of the deterioration of security in the Sinai, Morsi and his new military cadres sent hundreds of tanks, helicopters, other military equipment, and thousands of soldiers to the peninsula in order to fight the militant groups in a direct violation of the 1979 Egyptian-Israeli peace treaty, which called for severe restrictions on the number of Egyptian soldiers and military equipment to be deployed in the Sinai. Israeli newspaper Ha’aretz reported on Aug. 16 that the Israeli government bitterly complained to the U.S. about the lack of consultation by the Egyptians and their disregard in seeking their approval as stipulated in the treaty.

On Aug. 21, Israeli newspaper Ma’ariv wrote that what mostly disturbed the Israeli government was not the deployment of forces and equipment which it would have temporarily approved, but the fact that Egyptian officials are openly challenging the restrictions in the treaty, accusing the Israelis themselves of violating it many times before when they attacked Gaza. Other Egyptian politicians and senior MB leaders have also publicly vowed to re-assert complete sovereignty over the Sinai regardless of the treaty stipulations.

On the day of the military shake-up in Cairo, the U.S. government initially declared that it was surprised by Morsi’s decisions. The following day State Department spokesperson Victoria Noland said that the U.S. was aware of the pending shuffle but was surprised by its timing. In response, Ali, Morsi’s spokesman denied that anyone, let alone the Americans, knew or was informed of the sweeping decisions. So it is unlikely that anyone knew beforehand since clearly when both Secretary Clinton and Defense Secretary Leon Panetta recently visited Cairo, they met with Morsi and Tantawi in an attempt to mediate between the parties.

While the U.S. has publicly called for reinstating civilian rule and the restoration of presidential powers, the administration is very much concerned about the independent path asserted by Morsi. For many decades, Mubarak’s Egypt was a U.S. client state ready to support any dictate of U.S. foreign policy in the region. In addition, the U.S. gave the military an annual subsidy of $1.3 billion in order to maintain its leverage over this critical institution. Now, U.S. policymakers – to the detriment of Israel and its American supporters- have to be much more sensitive to Egyptian public opinion and its leaders’ insistence to assert their national sovereignty and independence.

But the first test of this new but complicated relationship has come soon enough. For years the U.S. government has meticulously tried to isolate Iran in the region. It recently called on Egypt not to restore its diplomatic relations with the Islamic Republic but to join a tacit regional alliance against it. American allies in the Arab world led by Saudi Arabia and the U.A.E. have surreptitiously conditioned their economic aid to Egypt on maintaining a hostile or cold attitude towards Iran. Despite all these pressures, President Morsi recently extended an extremely warm welcome to Iranian President Mahmoud Ahmadinejad when the two met last week during the Islamic Conference in Saudi Arabia. He subsequently announced a visit to China and Iran at the end of August despite the U.S. public displeasure over the visit.

Subsequently Morsi also announced that the only sensible way to address the crisis in Syria was not through the U.N. or NATO involvement, but through negotiations overseen by Egypt, Turkey, Saudi Arabia, and Iran, a bold move that combined the most important players in the region while ignoring all outsiders. On Aug. 23, theNew York Times reported that the U.S. and Israel were extremely concerned about such overtures between Tehran and Cairo and that such concerns will be at the top of the agenda when Morsi visits Washington at the end of September.

Since he became president many pro-Mubarak remnants and hardcore Shafiq supporters started a campaign of attacks and insults against President Morsi and the MB in an attempt to depose him and destabilize his nascent government. This campaign was manifested through many private media outlets that they controlled, including daily newspapers, magazines, and satellite channels. In one particular instance Islam Afifi, the editor-in-chief of the daily Al-Dostoor initiated a vicious campaign of lies, fabrications, and slander that were directed not only against Morsi but also his family. In Egypt, any citizen can file a criminal complaint to the state prosecutor who must investigate and decide on whether or not to prosecute. In this case the state prosecutor – who acts independently of the president- decided to prosecute.

Moreover, the law in Egypt also empowers judges to jail defendants prior to their conviction if there is a prima facie case against them. Once the trial commenced on Aug. 23 the judge ordered the immediate arrest of Afifi pending his trial. Within hours, President Morsi used his legislative powers and issued a law that banned the imprisonment of journalists because of their opinion not only pre-conviction but also post-conviction. The penalty in the new libel law is no longer criminal but civil. But if convicted, the defendant would have to pay a hefty fine. Because of the new law the editor was freed immediately, thanks only to the person that he has been deceitfully slandering for weeks.

While it took decades to curtail the influence of the army in running the country in countries like Turkey and Spain, Morsi was able to overcome it in a matter of weeks. But one should be under no illusion that the influence of the military in Egypt has disappeared. The Egyptian military is still a major player not only in foreign affairs but also in Egypt’s economy, possibly controlling as much as twenty to thirty percent of its GDP. The disengagement of the military from politics could prove to be much easier and smoother than extricating its economic interests so it can focus on its main mission in protecting the country. But Egypt’s modern military is a sixty year-old professional institution. And it is to the great credit of this institution that such dramatic changes took place without much rift or rupture within it.

By quietly reining in SCAF’s rule, Morsi was able to overcome his greatest challenge to date. Meanwhile, the pro-Mubarak remnants and their anti-Muslim Brotherhood allies trying to undermine his rule have mobilized in order to depose him on Aug. 24, while most revolutionary and nationalist groups have declined to join and condemned their rhetoric of insults and divisiveness. Although the movement to depose him will fizzle out, there is no doubt that Egyptian society is still divided over the role of Islam in public life. But this question will soon be answered as the Egyptian people will go to the polls again within the next six months in order to elect their representatives after they approve in a national referendum the new constitution that is currently being written.

But perhaps the foremost challenge facing the Egyptian president is how to assert real national sovereignty and independence in the face of tremendous pressures coming from all directions, foreign and domestic, in order to pull Egypt back to the U.S.-Israel orbit regardless of the will of the Egyptian people. That is clearly a challenge that cannot be overcome through issuing a presidential proclamation or ordering a reshuffle.

Esam Al-Amin can be contacted at alamin1919@gmail.com