The Brothers didn't start or organize the protests. That honor belonged to a loose coalition of leftists, democratic reformers, and Internet activists who used the murder of a young businessman by Egypt's thuggish police, and the example of Tunisia's own revolt, as the springboard for a history-altering uprising. The Brotherhood, fearful of a government crackdown as always, didn't even join the protests until the handwriting was on the wall.
But the Brothers knew they were Egypt's most popular and best-organized grass-roots movement and were perfectly poised to take advantage of a political opening. They grabbed the opportunity.
Now, 2-1/2 years later Mohamed Morsi, the man the Brothers propelled to Egypt's presidency, is under house arrest, and his allies swept from political office and influence by the military. Brotherhood news media have been shuttered and arrest warrants issued for the group's leaders. The same military that gave them their chance at power when it deposed Mr. Mubarak booted them from office in a second coup after protests that dwarfed those of 2011.
While the Brotherhood's opponents have rejoiced, a return to indirect military rule has roiled the country. Brotherhood supporters have taken to the street every day since July 3, when the Supreme Council of the Armed Forces (SCAF) appointed Judge Adly Mansour, a political neophyte completely unknown to the public, as interim president. Fifty Brotherhood supporters were gunned down by the military on July 8 and overnight clashes yesterday and today in Cairo between supporters and opponents of the deposed president left at least 7 dead. The Brotherhood has vowed to paralyze the city with ongoing sit-ins and protests until Morsi's rule is restored.
Egypt's current political chaos isn't entirely the fault of the Brothers, but in Egypt they're getting most of the blame – and certainly deserve the lion's share of it.
The dream was that that the founding movement of the modern Islamist project in its founding country would finally come to power and prove to the region and the world that political Islam works. But instead, Egypt became ungovernable as Mr. Morsi and his advisers alienated opponents, failed to build coalitions and treated a narrow presidential election victory as license to remake Egypt in their own image.
Morsi's failures as president brought the Brothers dream crashing down, at least for now, and raises troubling questions for the future of Egypt, and perhaps the region.
Generations of Brothers were told that political participation and gradual political and social outreach were the way to bring change to Egypt, a country where the precepts of Islamic law ultimately held sway. The group, founded in 1928, abandoned violence as a tool of change in the 1970s after decades of repression, including the assassination of its founder, Hassan al-Banna, in 1949, and the torture and execution of leading ideologue Sayyid al-Qutb by the Egyptian state in 1966.
But after the past month, many members consider the peaceful path to change blocked. They see the results of a presidential election that Morsi won fair and square in June 2012 being overturned by a military whose arsenal brims with weapons provided by the United States. That the US announced a delivery of F-16s would go ahead shortly after the coup was a data point of great interest to the Brothers, even if the failings of both Morsi and the organization were not.
Will McCants, a researcher at the Center for Naval Analyses in Alexandria, Va., who focuses on Islamist movements, says the worldview of jihadis – that violence is the only way to effect change without Western interference – is likely to be bolstered by recent events, while faith in the softer approach is likely to be eroded, at least among Brotherhood cadres.
Al Qaeda leader Ayman al-Zawahiri, an Egyptian doctor who fled his homeland decades ago, must be delighted with the turn of events, Mr. McCants says.
"What does the Egyptian Brotherhood learn from what's happening now?" McCants asks. "My worry is that they learn to be far more intransigent, they learn to more strenuously cultivate ties to violent actors so they provide a credible threat to their opponents and state security.… I worry that it's going to be a far 'harder' Brotherhood that emerges out of this."
It's not difficult to find that hardening if you attend a pro-Morsi demonstration in Cairo. Abdullah Shabaan spews his fury at the military, particularly army chief Gen. Abdel Fatah al-Sisi, who has been the public face of the military during the crisis.
"The coup is treachery, the biggest betrayal I've ever seen. Sisi took the side of hundreds of thousands of protesters, but ignores us. We're millions more," Mr. Shabaan says. "We haven't always agreed with Morsi's decisions, but now, especially after the coup and the massacre at the Republican Guard, we understand that there has always been a third party: the Army."
It's far too soon to write the obituary for Islamist movements. The Brotherhood in Egypt has proved adaptable in its 90 years of existence, as have its regional imitators.
Egypt hasn't been the only setback. In Turkey, prosperously ruled by the Islam-rooted Justice and Development Party for a decade, protesters have hit the streets by the hundreds since late May, complaining of attempts to forcibly Islamicize Turkish society and dictatorlike rule by Prime Minister Recep Tayyip Erdogan.
Not surprisingly, Mr. Erdogan was one of the few regional leaders who condemned Egypt's coup. "Coups are clearly enemies of democracy," he said. "We don't respect those who don't respect the people's will."
The current picture is mixed, McCants says. The Muslim Brotherhood may eventually even come to see its removal from power after only a year as a blessing, since it won't be held responsible for government failings going forward.
"This had to play out this way, but it's frustrating to me, as someone who is not a fan of the Islamist project, for Islamist rule of Egypt not to be allowed to completely fail on its own," McCants says. "I worry that the coup has kind of short-circuited the process of the Islamists kind of hoisting themselves by their own petard and demonstrating that the ideology isn't really fit for governance."
The regional winners may be the Salafis, even more conservative in their religious practice and more ideologically rigid. They are happy to wield influence as a political minority with a narrowly defined platform, removing the pressure to broaden their support base through compromise and deliver on promises.
The new political face of Islam may end up being more extreme than the one toppled July 3.
"What at first glance looked to be a real opportunity across the region for the Brothers, for one reason or another … they have lost ground," McCants says.
The days since July 3 have been turbulent. After the July 8 massacre Shabaan referred to, when soldiers gunned down about 50 people protesting Morsi's ouster, gruesome pictures of the dead circulated on Egyptian social media, as did video that appeared to show a soldier taking random shots at a crowd from a rooftop.
The violence goes both ways. Video showing a group of heavily bearded men, described as Brotherhood supporters, assaulting a cowering group of opponents and tossing them from a 30-foot ledge has also made the rounds.
Egypt's Coptic Christians, who backed the protests against Morsi, have also been targeted. In the upper Egyptian village of Nagaa Hassan, a local Christian businessman who had campaigned against Morsi was hacked to death by an ax-wielding mob July 5. The mob also burned dozens of Christian homes in the town and murdered three other people.
The violence has been scattered and rare, but it's a symptom of a broken Egyptian polity. Triumphant liberals and Muslim Brotherhood members viciously sling insults at each other, with both sides accusing the other of being tools of foreign powers out to destroy Egypt.
A spirit of compromise has been missing all along. Early Brotherhood assurances to those fearing Islamic governance, that it wouldn't seek the presidency or more than a third of the seats in parliament, quickly collapsed. After heated internal debate, the movement went for broke, contesting half the seats and throwing a presidential candidate into the ring.
Morsi eked out a presidential victory, with 51 percent of the vote, over Ahmed Shafiq, a former Mubarak loyalist, in part thanks to large numbers of secular voters calculating that a Brotherhood leader was a better bet for solidifying the revolution's gains than a hated felool, or remnant, of Mubarak's regime.
The huge protests in June and July were a demonstration of their buyer's remorse.
It's not hard to understand why. Morsi and his allies rammed through a constitution that carved out a role for Muslim clerics in determining the law, stifled criticism with a series of defamation suits that invariably focused on detractors of Islamist rule, and seemed more focused on Islamization campaigns than on the deteriorating economy.
Michael Wahid Hanna, a senior fellow at The Century Foundation in New York who has written about Egypt's political transition, says the Brothers clearly overplayed their hand. As a result, they could be left out in the political cold for quite a while.
Egyptian politics has four broad camps, he explains: Islamists like the Brothers, secular political groups ranging from Troskyities to liberal democrats, supporters of the former regime, and what Egyptians call the Hezb al-Kanaba – the "couch party" of people who are generally reluctant to get involved in street-level politics.
This last group clearly accelerated the protests, which drew the core of their strength from former regime supporters and reformers.
"For any mass movement in Egypt to make an impact, you need at least two of those components to be unified," Mr. Hanna says. "The divide between the Brotherhood and the rest [of political society] is so deep and profound now that you will never again see anyone from outside the Islamist camp throw their lot in with them to fight a common enemy."
The Brotherhood will be further hindered by fracturing within its own ranks, he says. Ahead of the protests and coup, leadership was deeply divided, with some urging concessions and others insisting that would be a sign of weakness.
Now the group is "essentially decapitated," Hanna says, with its leaders in jail and the rank and file uncertain of what to do. Backing away from protest and confrontation probably makes strategic sense now, but he worries that they may later go in the other direction.
Hanna isn't as worried as McCants about a return to violence, but that's not to say he's optimistic about a democratic transition happening anytime soon – he reckons hope for that is as slim as it was two years ago. He merely thinks the Brothers recognize that if they go to war with the Army, which is essentially the state at this point, they'll lose. Badly.
Egypt's politics is now a sort of Gordian knot, with the Brothers at its center. A meaningful political consensus can't be built without them, but it's hard to see how one can be forged with them, given the fury on all sides now.
In a letter calling for an independent investigation into both the massacre of Muslim Brotherhood supporters outside the military's Republican Guard office in Cairo July 8 and acts of violence elsewhere by Brotherhood supporters, a group of 15 leading Egyptian human rights organizations laid out the stakes.
"The continued incitement to bloodshed will make it practically impossible to re-launch a comprehensive political process leading to the fulfillment of the revolution's goals in Egypt," they wrote.
That incitement has not stopped yet. When, and if, it does will be an indication that Egypt can turn in a happier direction.
(This story was corrected after publication to correct the date of Qutb's death; he was arrested and imprisoned in 1954, but executed in 1966).
• Louisa Loveluck contributed reporting from Cairo.