The military found itself on the defensive after the bloodshed, but the interim president drove ahead with the army's political plan. He issued a swift timetable late Monday for the process of amending the Islamist-backed constitution and set parliamentary and presidential elections for early 2014.
The killings further entrenched the battle lines between supporters and opponents of ousted President Mohammed Morsi, who was removed by the military July 3 after a year in office following mass demonstrations by millions of Egyptians.
Morsi's Muslim Brotherhood called for an uprising, accusing troops of gunning down protesters, while the military blamed armed Islamists for provoking its forces.
The shootings began during a protest by about 1,000 Islamists outside the Republican Guard headquarters where Morsi, Egypt's first freely elected leader, was detained last week. Demonstrators and members of Morsi's Muslim Brotherhood said troops descended on them and opened fire unprovoked as they finished dawn prayers.
"I was in the last row praying. They were firing from the left and right," said Nashat Mohammed, who had come from southern Egypt to join the sit-in and was wounded in the knee. "We said, `Stop, we're your brothers.' They shot at us from every direction."
After a battle lasting about three hours, at least 51 protesters were killed and 435 wounded, most from live ammunition and birdshot, emergency services chief Mohammed Sultan told to the state news agency.
At a nationally televised news conference, Army Col. Ahmed Mohammed Ali said police and troops came under "heavy gunfire" at around 4 a.m. and attackers on rooftops opened fire with guns and Molotov cocktails. A soldier and two policemen were killed, and 42 in the security forces were wounded, eight critically, he said.
While he said troops had a right to defend the facility, Ali did not directly explain how the protester deaths occurred. He expressed condolences but offered no apologies for the deaths.
A collection of video of the clashes provided by the military to Egyptian TV showed protesters on rooftops lobbing projectiles at troops below, including firebombs and toilet seats. It also showed some armed protesters firing at close range at the troops, but it did not show what the military did. It was also not clear at what time in the fighting the videos were shot. It included aerial views of the clashes.
Several witnesses from outside the protest said the gunfire started when troops appeared to move on the camp.
University student Mirna el-Helbawi told The Associated Press that she watched from her 14th floor apartment overlooking the scene, after she heard protesters banging on metal barricades, a common battle cry. El-Helbawi, 21, said she saw troops and police approaching the protesters, who were lined up on the street behind a make-shift wall. The troops fired tear gas, the protesters responded with rocks, she said.
Soon after, she heard the first gunshots and saw the troops initially retreat backward -- which she said led her to believe the shots came from the protester side. She saw Morsi supporters firing from rooftops, while the troops were also shooting.
The Freedom and Justice party, the Muslim Brotherhood's political arm, called on Egyptians to rise up against the army, which it accused of turning Egypt into "a new Syria."
"This could be a moment of extremism for both sides" of the equation, Mohammed Mahsoub, a member of the Islamist Wasat Party told Al-Jazeera TV.
The sole Islamist faction that backed Morsi's removal, the ultraconservative Al-Nour Party, suspended its participation in talks on forming a new leadership for the country. The group is now torn by pressure from many in its base, furious over what they saw as a "massacre" against Islamists.
Reeling from scenes of bloodied protesters in hospitals and clinics, many with gaping wounds, some of Egypt's politicians tried to push new plans for some sort of reconciliation in the deeply polarized nation.
Sheik Ahmed el-Tayeb, the grand imam of Al-Azhar, the most prominent Sunni Muslim institution, demanded that a reconciliation panel with full powers immediately start work and that those detained in recent days be released. Five prominent Brotherhood figures have been jailed since Morsi's fall, and Morsi himself is held in detention in an unknown location.
El-Tayeb's announcement he was going into seclusion was a symbolic but dramatic stance -- a figure seen as a moral compass by many Egyptians expressing his disgust with all sides in the events. Egypt's Coptic popes have at times gone into seclusion to protest acts against the Christian community, but the sheik of Al-Azhar has never done so.
Struggling whether to fully bolt from the new leadership, the ultraconservative Al-Nour Party denounced what it called incitement against fellow Islamists. Speaking to Al-Jazeera TV, the party's chief Younes Makhyoun raised the possibility of calling a referendum on Morsi as a compromise measure.
There were multiple calls for an independent investigation into the bloodshed as a way to establish the truth and move forward.
The military-backed interim president, Adly Mansour, ordered a judicial inquiry into the killings. Significantly, the statement from his office echoed the military's version of events, saying the killings followed an attempt to storm the Republican Guard's headquarters.
The new leadership announced a fast-track timetable that would lead to elections for a new parliament within about seven months.
Under the plan, two panels would be appointed to made amendments to the constitution passed under Morsi. Those changes would be put to a referendum within about 4 1/2 months. Parliamentary elections would be held within two months, and once the new parliament convenes it would have a week to set a date for a presidential election.
The swift issuing of the plan reflected a drive to push ahead with a post-Morsi political plan despite Islamist rejection -- and is certain to further outrage the Brotherhood.
Egypt's escalating crisis could further complicate its relations with Washington and other Western allies, which had supported Morsi as the country's first freely elected leader and now are reassessing policies toward the military-backed group that forced him out.
Still, the White House said Monday that cutting off the more than $1 billion in annual aid to Egypt was not in the U.S.'s best interests, though it was reviewing whether the military's moves constitute a coup -- which would force such a measure under U.S. law.
But Egypt's new leadership appeared to be pushing ahead with the "road map" the military set up for the post-Morsi political system. Negotiations have been ongoing over appointing a prime minister, who will hold the main powers in governing the country. Talks have been stalled by Al-Nour Party vetos of candidates from liberal and secular factions -- but if the party drops out, those factions may push through a candidate.
At the same time, the military was pushing hard to isolate Islamists from public support, depicting their protests as rife with gunmen and weapons.
Ali said the sit-in outside the Guard headquarters had "abandoned peacefulness." Ali also pointed to other incidents of Islamist violence, including coordinated, deadly attacks by extremists on military installations in the Sinai Peninsula.
Prosecutors in Cairo also ordered the closure of the Brotherhood party's headquarters amid investigations into a cache of weapons found there, according to the official Middle East News Agency.
During the wave of protests last week that led to Morsi's removal, Brotherhood supporters used guns in several instances to defend their offices when opponents marched on them -- or outright attacked them.
Pushing ahead with the military "road map" is likely to further infuriate Islamists who have vowed to continue protests until Morsi is restored and now depict the military as willing to wipe them out by force of arms.
Outside hospitals and clinics near Monday's violence, Morsi supporters waved the bloodied shirts of the dead or wounded.
"The only thing the military understands is force and they are trying to force people into submission," said Marwan Mosaad, speaking at a field hospital run by Morsi's supporters. "It is a struggle of wills and no one can predict anything."
Abu Ubaida Mahmoud of Al-Azhar University said he had been praying when the sit-in's security teams began banging on metal barricades in warning. He then saw troops coming out of the Guard complex.
"The number of troops that came from inside was stunning," said Mahmoud, who was wounded in the hand.
It was "as if they were firing at an enemy," said another protester, Ahmed Youssef.
By the afternoon, the sit-in site was cleared along with blockades that had been set up on roads. The site of the early morning clashes, a strip of road about a kilometer long (about half a mile), was covered with rocks, shattered glass, shoes, clothes, prayer rugs and personal photographs.
A big Morsi banner remained hoisted in front of the Republican Guards' building. On the ground below it, graffiti read: "Where are our votes?"
Take ABC13 with you!
Download our free apps for iPhone, iPad, and Android devices