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Less than three years after the popular uprising that ousted Hosni Mubarak, the democratically elected government has been overthrown and the Egyptian military is running the state. GlobalPost and FRONTLINE have been on the street from the earliest days. GlobalPost's Charles M. Sennott again partners with FRONTLINE on the documentary “Egypt in Crisis” airing September 17, 2013 on PBS.

Egyptian Army al-Sisi supporters July 2013
Supporters of army chief General Abdel Fattah al-Sisi wave the Egyptian flag as an army helicopter flies over Tahrir Square in Cairo on July 16, 2013. Egypt's authorities formally detained Mohamed Morsi on suspicion of collaborating with Palestinian militants in murdering policemen and staging prison breaks, as tens of thousands of the deposed president's supporters and opponents staged rival rallies. (Khaled Desouki/AFP/Getty Images)

Four ways Egypt's military is enshrining the 'deep state'

Analysis: The generals who control Egypt have found subtle but troublingly effective ways to lock in power over civilians.

CAIRO — Amid the rise of General Abdel Fattah al-Sisi and the fall of the first democratically elected government in Egypt’s history, the military’s “deep state” has enshrined itself with a special status that will keep it immune from criticism or inspection and largely unanswerable to any civilian authority.

In short, the “deep state” is not going away any time soon and in many ways now runs ‘deeper’ through the core of the nation than it did even under the regime of deposed President Hosni Mubarak.

Here are four ways in which al-Sisi and the interim government appear to be further enshrining the “deep state” and why Egyptians and anyone in the world who cares about democracy should be concerned about this concentration of power:

1) Changing the army's creed and loyalty

Since the military appointed President of the Constitutional Court Adly Mansour as an interim president for Egypt last July, he issued two presidential decrees regarding the military.

The first decree was to increase the salaries of soldiers and pensions of retired officers, which is the second time military personnel received raises since the January 25 Revolution. President Mohamed Morsi, who was removed from power in July and remains in detention at an undisclosed location, took a similar decision at the beginning of his presidential term when he was working closely with the military leadership.

The second decree, issued in July, was known as “Number 562” and it change the military oath that officers recite during their graduation from the military school.

This new oath obliterated a longstanding phrase in the previous oath that bound officers to be "loyal to the president of the republic."

Future graduates of the military school will swear to protect the safety of Egypt inside and outside its lands, and to "obey the military orders, and execute the orders of the commanders." In other words, the military’s loyalty to the executive branch of a civilian government has been stripped away.

This stunning shift in loyalty by the military either went ignored by the Egyptian state-run media or was praised in print and on broadcast news. The reports often cite military experts who claim that the new oath is aimed to strengthen the loyalty of army to the country itself and its supreme interests, not to a certain individual.

Although the new oath emphasizes obedience to military orders and commanders, and ignores any subordination to a civilian authority, most Egyptians didn't realize the grave implications hidden in the semantics.

The corrupt regime of Mubarak and the failed presidency of Morsi have tarnished the image of civilian government and its authority in the eyes of the public. And both of these leaders, Mubarak and Morsi, served to strengthen the role of the military, to entitle it to become an economic powerhouse and to simultaneously shield it from civilian review. As a result, citizens of Egypt are skeptical of their elected government leaders while the popularity of the military is on the rise. Polling in Egypt consistently confirms that the military is by far the most trusted institution in the country.

The extraordinary pace of history unfolding in the last two and a half years seem to have blinded many Egyptians to the fact that a civilian president should be the only lawful representative to their collective will, and that the submission of the armed forces to a democratically elected leader is the only guarantee to keep a rogue general from abusing his power to enforce a political agenda.

Here is a hypothetical scenario that all Egyptians should consider given the vast economic empire over which the military presides: Imagine decades down the road, that Egypt will be ruled by a popular, powerful, civilian-elected president, who seeks to tame the enormous military budget. Specifically, how it should be allocated and whether the military should be investing in banquet halls, hotels and other civilian businesses.

When this hypothetical president tries to enforce any reforms in the military, he is going to be faced by three generations of army generals and commanders who were indoctrinated from their first day in training to be loyal to the military and its interests, not to a civilian authority. This will likely lead to a fierce political confrontation, or quite possibly another military coup to replace an