Egyptian president Mohamed Morsi’s housecleaning over the last two weeks—dismissing several top army officers and an intelligence chief and abrogating constitutional amendments limiting presidential power—has left observers trying to figure out the grand design behind Morsi’s actions. Some think it’s a “soft coup” against the remnants of the Mubarak regime, others lament that it signals the culmination of the Muslim Brotherhood’s victory over the army for control of Egypt, and yet others believe it is a first step toward civilian accountability in Egypt’s fledgling democracy. And now there’s a story circulating in the Egyptian media that the military leadership was ousted because it had plotted a coup against Morsi that he uncovered before it was too late.

For all the news reports there are still way too many shadows and hardly enough light to tell what it all means.

Gone from the highest ranks of the army are Field Marshal Mohamed Hussein Tantawi and armed forces chief of staff Sami Enan, along with the heads of the air force, air defense and navy. Tantawi was head of the Supreme Council of the Armed Forces and interim ruler of Egypt between Mubarak’s fall and Morsi’s presidency.

The army never wanted responsibility for governing Egypt, lest its extensive business interests come under scrutiny. Instead, the army wanted to exercise its power from the shadows. According to some sources, it may have been precisely the desire of the army’s senior leadership to prove its authority that led to its downfall.

The sensational news out of Egypt today is that Tantawi and others plotted to have Morsi assassinated at the funeral for 16 Egyptian border policemen killed two weeks ago by jihadist militants in the Sinai. When Morsi learned of the plot, presumably from some of the men he has now advanced, like the new minister of defense, General Abdel-Fattah el-Sisi, he got rid of Tantawi and Enan as well as head of the General Intelligence Directorate, Murad Muwafi. The spy chief seems not to have been involved in the plot, but having discovered it failed to brief Morsi directly and instead went to Tantawi with the information.

Another version of the story suggests that it wasn’t a thwarted coup that cost Tantawi and the senior leadership their positions but failed political brinksmanship. Again, the terrorist operation in Sinai and its aftermath seem to play a central part in the story.

Over the last week, the Egyptian army has been undertaking a large operation in the Sinai against radical Islamist groups that have come to dominate parts of the peninsula. The murder of the 16 Egyptian border policemen appears to have been what finally spurred the army to act, but sources explain that this operation had been planned, but delayed, for some time. Some say it may have been postponed because of the difficulties inherent in the operation, but others say it was for political reasons.

Amr Bargisi, a senior partner at the Egyptian Union for Liberal Youth, explains that he was told by senior Egyptian sources more than a month ago that “the top military brass had put off the operation until Morsi formed the government.” The idea evidently was that as defense minister, Tantawi would initiate a large-scale operation in the Sinai shutting down the corridors and perhaps even tunnels connecting Sinai to Gaza. This campaign would put Hamas on the spot and by extension embarrass Morsi and the Brotherhood as well, now portrayed not just as friends of Hamas but supporters of jihadi militants in the Sinai. As Bargisi explains, “Tantawi wanted to show that the president is irrelevant, that SCAF still runs the show when it comes to big strategic questions that concern the Americans and Israelis.”

The problem for Tantawi was that the rest of the army knew that the defense minister was to blame for sacrificing 16 Egyptian lives so that he could send a message to Morsi. “The army was happy to see him go,” says Bargisi. “They’re relieved.”

Indeed, the younger officers are apparently galvanized by Morsi’s decision to get rid of Tantawi. Morsi seems to have understood that the Egyptian military is not a pyramid so much as institution roiling with competing ambitions. If the top brass is on the face of things the most powerful, history shows that it is the younger officers—from Gamal abdel Nasser to the military cadre that killed Sadat—who are potentially most dangerous to anyone who would rule Egypt. For the time being anyway, Morsi has them on his side. 

All of Morsi’s new appointments owe their advancement to him. Tantawi’s replacement, the 57-year-old Sisi, previously filled a variety of posts in the Egyptian army. Like Sami Enan, he also has good connections in Washington, including with senior Obama administration officials, like counterterrorism czar John Brennan. Sisi’s tenure as military attaché in Saudi Arabia may have won him friends in Riyadh, which would benefit Morsi and the Brotherhood, whose relationship with the kingdom is often strained. The Wall Street Journal reports that Sisi is said to be sympathetic to the Brotherhood, but regardless of his political sympathies, what perhaps made him most attractive to Morsi was his last posting, as head of military intelligence.

The purpose of Morsi’s reshuffling is not exclusively to keep the army in hand, it is also to consolidate control over the security portfolio. With the firing of Muwafi, Morsi got rid of a Mubarak holdover who took the GID job when Omar Suleiman was named vice president shortly before Mubarak’s downfall. In his stead, Morsi named Mohamed Raafat Shehata. The president of Egypt needs the Egyptian army to wage military operations, but it is only the intelligence services that will keep him in power, or alive.

Perhaps, as some analysts have argued, Morsi’s personnel decisions show that he is “implementing a degree of accountability” not often present in Egyptian governance. However, his abrogation of constitutional powers granted to SCAF in the March 2011 has others concerned.

David Schenker at the Washington Institute for Near East Policy explains that in addition to the right “to appoint civilian and military employees and political representatives,” Morsi also “assumed powers granted to the SCAF under Article 56 of the interim constitution, including the right to ‘legislate’ … to ‘issue public policy for the state and the public budget and ensure its implementation,’ to ‘sign international treaties and agreements.’”

It’s this last clause that may be the most worrisome. “In addition to the right to sign treaties,” Schenker says, “Morsi presumably has the right to abrogate them, too. Since the Muslim Brotherhood is already talking about revising Camp David, a president now holding unchecked powers is troubling, to say the least.”

On the other hand, at this point in the game it would be very difficult for American policymakers to object to a revision of the constitutional amendments that essentially amounts to substituting the word “president” for “military council.” The Egyptian president has vanquished Tantawi’s SCAF, thanks apparently to the younger officers who bristled under the former defense minister’s leadership. But it is still too early to say whether Morsi has established once and for all civilian control of Egypt.

Who knows how much Morsi himself is calling the shots, or how much is done in consultation with Muslim Brotherhood leadership, and the man likely to be named deputy prime minister, Brotherhood strategist and millionaire Khairat al-Shater. Perhaps the army will once again be happy to recede into the background where it is most comfortable managing its business interests. In any case, it is only the top, and perhaps most vulnerable, layer of the Egyptian army that lost this round. Should competition between the army and the country’s first civilian president resume, it will be once again for control of the street as well as the shadows, where power in Cairo resides.