Since 1952, Egypt has been run by the military. By that we don't just mean that it was headed by a president with a military background. The military is involved in more aspects of civilian life than many would imagine. Some estimate that the military runs about 40% of the Egyptian economy in the form of companies, factories, farms and construction companies. We also know that they had a say in permitting (or prohibiting) the use of certain technologies (communication, GPS and others). The determination of the use of any land across the country had to be approved by the military, resulting in some cases in the army reserving some of the most prime plots to its own use. In addition, key positions in the government such as: governors, heads of government influential agencies and presidents of public companies, were given to ex-generals. Moreover, the army has a major role in many of our bilateral relationships with the outside world. In short, the involvement of the army in the decision making in this country stretched far beyond their traditional role of protecting our borders.
In the 5 – 7 years leading up to January 25, Mubarak had largely left the decision making to the NDP headed by Gamal and his cronies. The move was a clear indication to the army that the country was heading towards a civilian rule. The management of the country at that time was split in two, the old guard (including the army) and the new guard (Gamal's group). While the new guard worked on the economic side, the oldies worked on the security aspects, they maintained control over such ministries as Defense, Interior, Foreign Affairs, but also on what they considered security threats such as Ministry of Solidarity, Employment and Education. The separation between the two camps has lead to several cracks and a chaotic government policy. Whereas, such conflict has resulted in the big mess we've witnessed in the past years, it has also prepared the army to a certain extent for an eventual change in its involvement. Needless to say that the army did not like that scenario one little bit, especially that they probably saw that Gamal neither had the strength of character nor the vision that they would've liked to see in an upcoming leader. Several discussions about an eventual coup must have taken place behind closed doors with the option to revert to a military dominance.
The revolution started on January 25th and put the army in an awkward position. On one hand, the end of the Mubarak succession plan came as a relief to them, but on the other hand, the fact that Egyptians took to the streets in millions to change their leader made them realize that reverting back to a strictly military rule was going to be very tricky. At first they tried to wrap it up by making minor cosmetic changes in order to maintain status quo: amending a few clauses in the constitution, removing some of the key figures in the ministries, etc. In doing so, they needed to ensure some popular support: who is more prepared to offer such support than the well organized, 82 year old Muslim Brotherhood? Not only are they the only ones capable of mobilizing large numbers but they are also the ones that, should they be allowed to gain control of the upcoming parliament, would happily draft a constitution that would retain a significant portion of the army's role.
The protests continued beyond the referendum and they soon realized a few things: 1) That there is no turning back from a fully civilian rule, 2) that the MB's are not as reliable as they thought they were, 3) that the country is not as manageable as they believed it was when they took over and 4) that there are far more socio-political forces in the country than just the MB's.