In fact, the army had not really left the political scene since Morsi dismissed the defence minister and head of the Supreme Council of the Armed Forces, Mohamed Hussein Tantawi, and Chief of Staff Sami Anan, in August 2012. Under the latter duo, the army had first run the country since the fall of Mubarak, in a transition period of 16 months, and then, after the election of Morsi in June 2012, wanted to maintain an extremely dangerous duality of civil-military power that would inevitably lead to a collision between the presidency and military institution. This confrontation was quickly ended, against all odds, with the dismissal of Tantawi and Anan less than two months after the inauguration of Morsi.
Since the appointment of the current defence minister, Abdel-Fattah Al-Sisi, to replace Tantawi, everyone thought that the army returned to its barracks. Al-Sisi himself does not want the army to play a political role. He was aware that its interference in politics during the transition period seriously tarnished its image and reduced its prestige among the population. The army, under Al-Sisi, would therefore merely preserve its multifaceted privileges. This was done in the new constitution approved last December. In addition, Morsi tried a rapprochement with the army to ensure its support in his conflict with the liberal opposition.
The army command remained nevertheless suspicious of the intentions of Morsi and the Muslim Brotherhood and opposed to their policies. This involved attempts to infiltrate or to “Brotherhoodise” the army. The rumour was so persistent that Al-Sisi had to reply on 14 February stressing that he would not allow the Muslim Brotherhood, or any other political group, to dominate the army. The command was also unhappy with criticism from leaders of the Brotherhood, including Supreme Guide Mohamed Badie, on past military support for the Mubarak regime.
On the other hand, the religious and sectarian dimension of President Morsi's policies was inconsistent with the strategic thinking of the army on national security issues. This involved first the rapprochement, by religious affinities, with the Islamic resistance movement Hamas in Palestine, which controls the Gaza Strip and adopts armed struggle against the Israeli occupation. For the army, this rapprochement is extremely dangerous for the security of Egypt, especially for that of the Sinai Peninsula, which occupies a particularly important place in the strategic thinking of the army, because it borders Israel and the Gaza Strip.
This region is considered the east frontier of Egypt, the source of the most serious threats to its security. The army was carrying, at least partially, the responsibility of the security vacuum and increased threat of jihadists in Sinai, in connection with Palestinian militants, since the fall of Mubarak, to the laxity of political power with Hamas and Islamist groups in this province.
The army was also dismayed by the support of Cairo to the idea of Islamic jihad against the regime of Bashar Al-Assad in Syria. This position, announced with great fanfare by Morsi 15 June, was dictated by the needs of rapprochement with Egyptian Salafists to counter the growing pressure from internal opposition. It went up to encouraging Egyptians to join the armed rebellion against Damascus. The army considered it a thoughtless and reckless policy that will have a very negative impact on the security of Egypt after the return of Egyptian jihadists to the country, as was the case with the "Egyptian Afghans" who fought Soviet forces in Afghanistan, and fed after their return to Egypt a wave of terrorist attacks in the 1990s.
What aggravated the case of Morsi in the eyes of the military was a series of errors in its handling of the affairs of the country, some of which directly related to the army. This was the case with the opposition and popular protests on the occasion of the 1st anniversary of the January 25 Revolution. The president asked the army to impose a curfew in the three cities of the Suez Canal region — Port Said, Ismaïliya and Suez. Upset by this policy of confrontation with the population and wanting to avoid the same and stay away from the maze of politics, the army said it would not use force against inhabitants of the three cities to impose a curfew, which was massively violated by the population to the chagrin of Morsi.
The multiplication of errors related to domestic policy ended up by completely turning the army against Morsi, pushing it to intervene to overthrow him. This series of episodes of serious misconduct and mismanagement exacerbated divisions in society, increased popular discontent and worsened political and security instability. A situation that greatly worried the military. The army's given mission is to preserve the territorial integrity of Egypt, but also its civil peace. It sees itself as the last bulwark against any external or internal threat that could lead to the collapse of the state.
Al-Sisi had already threatened different political players, including the president, on 29 January with possible military intervention if they failed to resolve the political crisis that could cause the collapse of the state.
The exacerbation of tension, which culminated in the giant protests of 30 June and after, led the army to decide to intervene. These massive demonstrations gave it the popular cover to overthrow the president. Al-Sisi tried during this particularly turbulent period to push Morsi to accept the demand of protesters for snap presidential elections. His refusal sentenced him to a showdown with the army, which dismissed him on expiry of its 48-hour ultimatum.
Drawing lessons from the previous transition period, where it was under fire from critics because of its direct management of the affairs of the country, the army this time highlighted the civil forces it has entrusted to form a new government and asked the head of the Constitutional Court to assume the presidency in an interim capacity. The army, however, remains the sponsor and guarantor of this new transition period, during which its influence will remain decisive. The extent of its future political role will depend on the result of the transition process.