The Brotherhood appeared to be caught flat-footed by the eruption of protests a week ago, fueled by young, more secular activists, and was slow to join in.
But once it did call out its membership, the result was that Alexandria saw the largest protests - and the fiercest clashes with police - of any city in Egypt, with tens of thousands marching through the streets, a sign of its organizing prowess.
Still, though it can bring out the sheer numbers, the Brotherhood is reluctant to present itself overtly as a leader or driving force in the protests, realizing that storming out with its hard-line slogans of "Islam is the solution" would disillusion secular groups, raise panic that it is trying to take over and bring a harsher government crackdown.
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"This is a people's revolution and it doesn't belong to the Brotherhood," said Amir Hussein, a 19-year old Brotherhood member who was among those in the streets of Alexandria over the weekend - the rhetoric echoed by many others in the movement from its lower ranks to upper leadership.
The question now is how the Brotherhood will deal with other opposition groups as the protest movement tries to coalesce and push through its demands that President Hosni Mubarak step down and his ruling party end its monopoly of power in Egypt. Particularly unclear is how it will relate with prominent reform advocate Mohamed ElBaradei, who some secular protesters are presenting as leader of the movement.
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A leading Brotherhood figure, Saad el-Katatni, said Sunday that the group was talking to other opposition to form a committee to direct the protest movement. ElBaradei would be a member of the committee, but not necessarily its leader unless the members elect him, el-Katatni said.
The Brotherhood, which calls for Islamic rule in the Arab world's most populous nation, is widely recognized as the best organized opposition movement in Egypt. Even though it's officially banned, it has a grassroots organization across the nation and disciplined followers. That has made it the most rival most feared by the regime of President Hosni Mubarak, which has cracked down repeatedly on the group in recent years, arresting hundreds.
But its elderly, secretive leadership can at times be deeply cautious. And when protests first erupted on Jan. 25 in Cairo and other cities, driven by pro-democracy activists largely operating on the Internet through social networking sites, the group stayed on the sidelines.
When the size of those protests stunned the nation, the movement was in danger of being left behind and changed its tune. said Alexandria journalist Ahmed Aly, who closely follows the group.
"The membership saw that it was the regular Egyptians going into the street and facing the battles, the Brotherhood felt like it couldn't miss the opportunity," said Aly.
The leadership encouraged its followers to hit the streets, though it did not officially join in as a movement. "We are encouraging people to take part, but our leadership will not be present," Ahmed Morsi, a Muslim Brotherhood spokesman in Alexandria, said.
After weekly prayers last Friday, tens of thousands spilled into the streets of Alexandria, calling for the end of Mubarak's rule. Clouds of tear gas billowed, fistfights broke out between protesters and riot police, and after hours of street battles, police retreated leaving nearly 100,000 people marching all day.
In protests Saturday and Sunday, Brotherhood members were the clear majority. With the Internet shut down, Brothers went house to house telling each other where to gather the next day, guaranteeing huge numbers on the street. At least 50,000 gathered in front of the unknown soldier statue overlooking the Mediterranean sea on Saturday, with a major Brotherhood contingent. There was celebratory feel to the demonstration, with people hugging and congratulating each other. People posed with army tanks that were sprayed with anti-Mubarak graffiti and handed their children to the soldiers for photos.
On Thursday night, the group said 30 of its Alexandria leadership were arrested, including prominent former parliament member Sobhi Saleh. The Brotherhood said they received threats of more arrests if they took to the streets but that didn't seem to deter them.
On Sunday, Saleh was among many prisoners who escaped early in the morning and was given a hero's welcome at the Alexandria protest. Thousands marched through the downtown core of Alexandria, with supporters carrying Saleh on their shoulders amid cheers and whistles. A small crowd of non-Brotherhood protesters turned away, looking obviously displeased with the extra attention the prominent Brotherhood member was receiving.
The strong Brotherhood presence in Alexandria marches was a contrast with those in capital, Cairo, where Brotherhood members were generally not overt in the participation until Sunday. Their appearance among the thousands camped out for days in Cairo's central Tahrir Square raised the suspicion of some secular protesters, who worried that the rallies could start to take a more fundamentalist look.
So far that hasn't happened. For the Brotherhood, being part of a wider movement with other groups has its benefits, giving it a degree of legitimacy - but that means not pushing its ideology or agenda too hard.
"The Brotherhood have not been out with their own slogans and banners," said Abdel-Galil el-Sharnoubi, who runs the Brotherhood website. "We have all agreed on a populist stance."