CAIRO, Egypt — If Egypt’s Muslim Brotherhood thought the military establishment was safely out of politics, the army is right now proving the Islamists horribly wrong.

In a stunning turn of events, on Wednesday Egypt’s military again seized some of the levers of state power, including the state television building, in what many are calling an army coup to push Brotherhood president Mohamed Morsi from power. 

Defense Minister Abdel Fattah al-Sisi issued an ultimatum Monday for rival political groups to resolve their differences as millions took to the streets to call for an end to Morsi's rule, after a period plagued by deep political polarization, civil strife and economic malaise in the year since he took power. 

This week's dramatic moves come on the heels of a brief era of rapprochement between the army and the Brotherhood in the wake of the uprising that toppled former President Hosni Mubarak. But the history between these two traditionally rival powers is too bloody and too deep. The current showdown will likely exacerbate these historical tensions, if not lead to fresh violence.

"The transition process has not led to a stable outcome,” Nathan Brown, Egypt expert and professor at George Washington University, said in an email interview of the period following Mubarak’s ouster. “And the military seems determined to erase the board and start over again.”

In the weeks after Mubarak’s fall, the Brotherhood tacitly agreed to support the constitutional amendments proposed by the then-ruling Supreme Council of Armed Forces (SCAF), and helped deliver victory to a snap referendum on the document. The amendments laid the groundwork for what proved to be a turbulent — and still unfinished — transition.

Brown says the supposed collusion between the Brotherhood and SCAF to marginalize more revolutionary forces was in fact overblown by secular and liberal parties that opposed the transitional road map.

While the Brotherhood failed to endorse mass protests against SCAF rule, the army also crippled the movement’s ability to legislate from parliament.

In June 2012, following an election runoff between Morsi and pro-military candidate and Mubarak-era prime minister Ahmed Shafiq, SCAF issued a second constitutional declaration that restricted the incoming president’s powers.

Two months later, Morsi canceled that declaration and forcibly retired the army’s two top generals. He then appointed current defense minister Sisi.

To almost everyone's surprise at the time, the generals appeared to have gone quietly.

The Brotherhood, having won parliamentary elections in 2011, later led the drafting of the constitution that safeguarded the army’s economic and political prerogatives, including its vast business holdings.

"I cannot imagine they [the military] could ask for anything more,” Brown said. “The [constitution] protects military trials and prevents real civilian oversight.”

More from GlobalPost: Egypt's military enters the fray, but its political role remains unclear

It was widely thought that Sisi, the new defense minister, had sympathy with strains of Islamist thinking — and that the army and the presidency would coordinate more closely.

But Sisi, too, imbibes much of the military’s “savior of the nation” thinking, said Robert Springborg, an expert on Egypt’s military and professor at the Naval Postgraduate School in Monterey, Calif.

“Much of the officer corps hates the Brothers, so Sisi has to be mindful of their views," he said. Sisi is currently crafting the military’s re-entry into politics.

It is true that military culture tends to view the Brotherhood and its Islamist vision as crude, and sees their decades-long position as an illegal dissident organization as subversive and disloyal to the state.

These sentiments have their roots in the 1952 coup led by the Free Officers, a secret organization within the military led by Gamal Abdul Nasser, later Egypt’s president.

Nasser and the Brotherhood, which was established in 1928, quickly fell out. The Islamists backed General Mohamed Naguib, the official head of state who was then locked in a power struggled with Nasser.

After a Brotherhood member attempted to assassinate him in October that year, he crushed the movement, arresting and torturing its members.

Under subsequent President Anwar Sadat, in the 1970s, the Islamists slowly began to emerge from the shadows. They still operated clandestinely, but were later tolerated by Mubarak, who let them run as independent candidates in parliamentary elections, as well as carry out charity work.

Morsi’s presidency offered the movement a chance to put its Islamist project into action. But a combination of poor governance, resistance from state institutions that still saw the Brotherhood as an enemy, and an ailing economy meant Morsi’s tenure was largely a failure.

The Brotherhood “are tone deaf to anyone or anything outside their organization,” Springborg said. "They resent anyone infringing on what they see as their right to decide."

In the past month, the strength of the street opposition to Morsi seemed to swell with each passing day, which brought Sisi and his fellow officers to the conclusion they should intervene, analysts say.

With the history of persecution and arrests casting a long shadow, Brotherhood members have in the last few days vowed to sacrifice their lives in the event of a military coup.

The relationship between the Brotherhood and the army was "always sensitive and difficult,” Springborg said. It’s “now impossible.”

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