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Families had stockpiled food and water, drivers had slept nights in petrol lines that snaked for city block after city block, and half a dozen people had died in a days-long spasm of violence that exploded into a full-blown seizure on Sunday, when mass protests against President Mohamed Morsi broke out and brought out  the largest crowds in Egypt's modern history. The headquarters of the Mr. Morsi's Muslim Brotherhood were set on fire on Sunday night, after offices of the Brotherhood's ruling Freedom and Justice Party were attacked and burned throughout the Nile Delta. Brotherhood toughs have banded together outside their offices wearing hard hats and makeshift shields and carrying homemade guns, ready to bludgeon or blow away what they fear is the very embodiment of the counter-revolution.

One online commentator described the mass movement to oust Mr. Morsi on the anniversary of his election – a movement known as Tamarod ("rebel") – as the birth of a new political order that may kill its mother. A journalist said it was as if Egypt's body politic were rejecting a transplant and killing the nation in the process, a fledgling democracy's auto-immune system gone haywire.

How did the country get here? How did the January 2011 uprising and its young, made-for-TV activists spin out into another zero-sum game for control? The story is complicated, and the strategic and tactical failures by both the secularist opposition and the Muslim Brotherhood are so profoundly, majestically short-sighted and self-defeating that some have retreated into that most time-tested of rationales, the conspiracy, to explain how things could have gone so wrong, so fast. In their narrative, the crisis has been stage-managed by the military, Egypt's eminence grise and ultimate power-broker, beginning on the day in February 2011 when the generals opportunistically seized on the mass protests to quietly but forcefully escort President Hosni Mubarak, his family and his cronies from the stage.

Like most conspiracy theories, the story has a seed of truth. In the heady days before and after the fall of Mr. Mubarak, the generals were taking everyone's temperature. At one time or another, they chatted with many of the revolution's most prominent instigators. They met with Ahmed Maher of the April 6th Movement. They met with representatives of the Brotherhood. Mohamed Aboul Ghar, who would soon found one of the only serious non-Islamist political parties in the country, once told me how he, the editor of Al Ahram newspaper, and two other men were called before five generals that March. One kept notes as they spoke; he was Abdelfattah el-Sisi, later promoted to defence minister and military commander-in-chief under Mr. Morsi. As the meeting adjourned, one of the generals casually remarked that the Supreme Council of the Armed Forces -- the military's governing body -- had in 2010 held a meeting without Mr. Mubarak, their commander, and decided not to allow the president's son, Gamal, to complete a widely telegraphed succession during rigged presidential elections then scheduled for 2011.

"The plan [was], when Gamal is going to take over, they are going make a coup," Aboul Ghar recalled. The military's disdain for Gamal and his generation of casually corrupt businessmen was well known, as was their desire not to see him crowned, and the January uprising provided a perfect opportunity to abort the Mubarak family dynasty. But after it became obvious that the masses would not accept a handover to Omar Suleiman, Mr. Mubarak's last-minute vice president and intelligence chief, the military needed a placeholder. Picking out a suitable figure from Mr. Mubarak's old National Democratic Party network would be impossible -- not in the aftermath of a rebellion that left their headquarters smoldering, their party dissolved, and their leaders facing prosecution. Egypt's political opposition, meanwhile, had been carefully neutered and co-opted for five decades; it had no base and its leaders no respect on the streets.

The only suitable dancing partner was the Muslim Brotherhood, an institution whose organizational, bureaucratic and service-providing experience was deeper than even that of the post-1956 militarized government itself.

And so the transition proceeded under military rule, directed by old, conservative men who learned their craft in a much different Egypt, half of them hoping to protect the old order, the other half pushing their project to usher in a new one. A temporary constitution orchestrated by the military and backed by the Brotherhood and their ultraconservative allies passed easily. Calls from figures such as Mohamed ElBaradei to create a liberal, progressive and inclusive new constitution from scratch, written by an independent body chosen by consensus, were ignored. As the year dragged on, poor Egyptians remained poor, and Mr. Mubarak sat uncharged with any crime in a military hospital. Protests against the military's reluctance to hand over power grew. They were supported by the Brotherhood, which likely saw in the unrest a useful tactic to keep their prime opponent on the back foot. In November 2011, the protests threatened to get out of control.

Security forces stormed Tahrir Square and brutally dispersed a small sit-in of a few hundred people -- almost all of them relatives of the revolution's martyrs or those who had been wounded. They had been forgotten by the state, and they were angry. The revolutionaries were infuriated at the attack, and the result was the battle of Mohamed Mahmoud Street, a five-day brawl with the riot police near the Square that left more than 40 civilians dead. The end of the fighting was precipitated by army intervention, the construction of a large concrete wall, and the arrival of a human chain of Muslim Brothers who cajoled or forced the protesters off the street.

The revolutionaries and marginalized young men and women who had joined the fight were filled with righteous anger. They felt betrayed. They had shed blood, supposedly on principle: to force police reform, to snatch some justice for those who had lost sons or daughters or their own health during the revolution, to hold the army to account for abuses under its rule. To them, the Brothers had thrown it all away for political gain. The temporary constitution had paved the way for parliamentary elections, due that month, a critical step that would help decide who ruled post-revolution Egypt. The Brotherhood could not let them be delayed. They went on to dominate the vote. Mohamed Mahmoud cleaved a rift between the two sides that never healed.

Over the course of the following months, it became obvious: The Brotherhood was dutifully, purposefully playing for keeps. Under the temporary constitution they helped to pass, the new parliament would be tasked with choosing those who would write a permanent founding document for post-revolution Egypt -- the holy grail. The Brotherhood would go to almost any lengths to secure it. But what they saw as predictable hardball and democratic combat -- which they were almost guaranteed to win -- the opposition saw as a series of betrayals.

The Brotherhood ran for more seats in parliament than some of their prominent members had first promised, then dominated the ministries once elected. The opposition hardly contested the second legislative election, for the less-powerful upper house, which was similarly dominated by the Brotherhood and Salafi parties. When the time came to select the constituent assembly, the Brotherhood's parliamentary bloc helped gerrymander its 100-member makeup so that if push came to shove, the Brotherhood and its backers would not be outvoted. The Brotherhood pledged not to seek the presidency, then fielded a candidate, and fielded another – Mohammed Morsi -- when the first was disqualified.

After Mr. Morsi took office, he failed to form -- or could not find those willing to join -- a cabinet that some had hoped would involve figures from across the political spectrum and prompt a national reconciliation. The Brotherhood, meanwhile, felt battered by the forces of the old regime. In the days before Mr. Morsi's victory, the Supreme Constitutional Court used an electoral technicality to annul the lower house of parliament, erasing the Brotherhood's gains and the country's most crucial elected body. The court docketed a case to rule on the legitimacy of the constituent assembly. Other courts planned to rule on the legality of the Muslim Brotherhood itself. Their entire project was now at risk.

The beginning of the end came in November, almost a year to the day after the Mohamed Mahmoud Street battle, when Mr. Morsi issued a package of sovereign decrees -- just four months into his term -- that essentially placed himself and the assembly above judicial review. He and his allies argued that to stand by and do nothing would leave courts packed with Mubarak appointees free to undermine every step of the transition. The opposition, which may have once been inclined to agree, did not take his side. There had been too many betrayals; trust had evaporated.

Protesters took to the streets, calling the president a "new pharaoh." The remaining liberals, progressives, leftists and Christians in the constituent assembly walked out. Mr. Morsi gave them two extra months to resolve their differences, but the assembly rushed the draft constitution through an overnight session and passed it. Opposition politicians increasingly believed that Mr. Morsi did not even call his own shots -- that decisions of national import were made in the Brotherhood's secretive Guidance Bureau. In Egypt's new constitution, human-rights groups and other critics saw gaping loopholes, lax protections for minorities, women and children, and troubling roles for religious oversight from conservative Sunni institutions.

The November crisis awakened the opposition to a harsh reality: they were going to keep losing this game, and the Brotherhood was not going to stop playing. The only solution was to change the rules. They united, for the first time, under the banner of the National Salvation Front. Their faltering effort to boycott and then vote down the new constitution failed, but the unexpectedly tight result convinced them that Mr. Morsi's base was shrinking. Soon after, the NSF declared that it would boycott upcoming parliamentary elections unless many of the rules -- written by the nearly wholly Islamist upper house -- were changed. Improbably, despite being filled with inflated egos and parties highly opposed to one another, the NSF held its front.

In December, after Morsi supporters ransacked a small sit-in outside the presidential palace and sparked deadly street battles, a more extreme wing of the opposition began to wield influence inside the coalition. They argued that Mr. Morsi had lost all legitimacy. He would have to go, voluntarily or by force. Violent anti-Brotherhood protests became the order of the day. Instability worked in the opposition's favour. The economy was nose-diving, and security forces -- becoming more openly vocal in their disdain for the Brotherhood government -- could not or would not do their jobs. Social media and independent television stations lit up with images of Brotherhood members beating away protesters. Newspapers openly mocked Mr. Morsi's government for its inability to right the ship. Rumours and anonymously sourced news reports spread about the Brotherhood's ambitions to Islamize the army and police and carve off critical swaths of sovereign assets, such as those along the Suez Canal, to sell to benefactors in Qatar. Mr. Morsi – one of the more deeply uncharismatic leaders in modern Arab history – proved incapable of rallying anyone outside his base.

The Brotherhood's majoritarian behavior had, by then, convinced many secular-minded Egyptians that Mr. Morsi and his administration would not engage in any meaningful negotiation. The goal for many in the opposition became the end of the Brotherhood's entire project itself.

Ministries were in quiet bureaucratic rebellion. Lower-level employees stalled paperwork. Mr. Morsi and the Brotherhood had, by now, almost fully retreated to their core supporters. He held a sectarianism-fueled stadium rally where he severed relations with Syria's Bashar al-Assad – after his administration had encouraged Egyptians to go fight in the war.

As the swamp of a long summer and economic decline loomed, the NSF waited. Then, in June, came Tamarod.

The Tamarod ("Rebel") campaign has publicly put into simple terms what many in the political opposition have been thinking for months: Morsi is the target, he must go. And when he goes, the Brotherhood project ends. The constitution is rewritten; the country presses the reset button on the transition.

Egypt is more polarized than at any point since the revolution. Figures from the old regime – Omar Suleiman's aide, the son of one of the Nile Delta's longtime Mubarak power brokers – have re-emerged to rally supporters against the Brotherhood. The irony is not lost on many of the most dedicated revolutionaries, who wonder whether their causes have been hijacked and their voices marginalized once again. Others have set aside such concerns, saying the Brotherhood represents the more clear and present danger. The enduring legacy of Mr. Morsi's presidency, if he does not survive his four-year term, may be his inadvertent facilitation of the counter-revolution.

If Mohamed Morsi falls or steps down, millions of Egyptians will view it as a victory. Perhaps he could be succeeded by a salvation government, and some kind of stable progress will ensue, though the Brotherhood can hardly be expected to quietly allow their project to dissolve around them, and it would likely mean the return of the army to a guiding role.

Revolutions come with chaos. History teaches us that many years may pass before a country comes out of such upheaval with a working government, satisfactory justice and reconciliation, and a consensus about national identity. But even in such a positive scenario, it is hard not to view the first two and a half years of Egypt's revolution as a series of squandered promises.

Evan Hill is a Cairo-based journalist. He tweets at @evanchill. A version of this article was first published on