On Friday, its leaders said they won't run a candidate for president, but the brotherhood does expect to play a role in Egypt's future, CBS News Correspondent Mark Strassmann reports.
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Long before the clamor of Tahrir Square, Hosni Mubarak heard one group's dissent and despised them for it.
They're the Muslim Brotherhood, religious conservatives, often secretive and poorly understood. What is clear: They want an Egyptian Islamic state. This week, they stepped out of the shadows and joined the protesters demanding Mubarak to step down.
"For so long we have voiced our rejection of these criminal policies which have spoiled all aspects of life in Egypt and all those who sought to express their opinion," the Muslim Brotherhood's deputy director, Dr. Rashad Albayomi, said.
The brotherhood, formed in 1928, is the world's oldest and most influential Islamic movement and Hosni Mubarak's sworn enemy.
Illegal in Egypt but tolerated -- to a point -- its members are frequently harassed and arrested by Mubarak's state police.
As a social charity, the brotherhood's won over many Egyptians, and in 2005 they startled Mubarak by winning 88 legislative seats, about one-fifth of Egypt's parliament. But last year, they boycotted and lost every seat in Mubarak's rigged elections.
The brotherhood rejects violence with certain exceptions, and for that groups like Hamas and al Qaeda have denounced them.
But even here some critics worry the group's possible political rise is a gateway to Islamic extremism.
Fiercely pro-Palestinian, some hardcore members want Israel wiped off the map while others strike a more moderate tone.
Jon Alterman is a Middle East expert and analyst for the Center for Strategic and International Studies in Washington.
"What's most scary about the brotherhood is that we're not really sure how, if at all, they would change were they to come to power or were they to even rise in power," Alterman said.
But whatever their political ambitions, Egypt remains a secular country, and most Egyptians want to keep it that way.
Under the agreement struck Friday, the brotherhood would have to be satisfied with any seats in parliament that they could win in the next election, but they would not be allowed to have any of the most powerful positions in the new government. This proposal, though, still has to be agreed upon by lots of parties, and there are lots of deep suspicions about the brotherhood and what their long range intentions are.