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Many fled to the oil-rich Gulf region where some built businesses that later proved crucial in helping the group reorganize in the 1970s. It had mixed fortunes under the 29-year rule of Mubarak, who jailed many Brotherhood members but looked the other way when they fielded ostensibly independent candidates in parliamentary elections.
Mubarak's 2011 ouster allowed the group to regain legitimacy and it went on to win every election since, capping those victories with Morsi's ascent to the presidency by a narrow margin. But a series of serious missteps, including an ill-fated attempt to place himself above any kind of oversight, concentrating powers in the hands of the Brotherhood and failing to solve any of the nation's pressing problems, sparked a wave of anger that saw millions take to the streets in June to demand that he step down.
It's not at all clear whether the group, despite being highly disciplined and organized, can recover from the latest crackdown. Insiders say it has already decentralized its leadership because many are detained or in hiding, and meetings often fail to come up with any decision on continuing street protests amid fears of arrest or violence.
The military-backed government has reinstated security officers who had spent years following the activities of religious groups, including the Brotherhood, under Mubarak, lending their expertise and knowledge to the ongoing crackdown, officials said. These officers have capitalized on the wave of popular resentment of the Brotherhood to go after mid-ranking members, arresting many of them, the officials said, speaking on condition of anonymity because they were not authorized to speak to the media.
"The Brotherhood will become a secret organization, will go underground once again and join ranks with extremist organizations," predicted Raafat Sayed Ahmed, head of the Yafa Center for Arab studies, a liberal think tank. "Younger members will take up arms against the government and you will see an armed secret organization in Egypt."
Still, he predicted the group will continue to show a measure of resistance so long as its sources of funding are left untouched by authorities. "The blow of death is when the money dries up," Ahmed said.
He, like others, predicted the Brotherhood will join an insurgency already under way in the Sinai Peninsula by extremists sympathetic to the group, while simultaneously starting another in southern Egypt, where the Brotherhood and Gamaa Islamiyah, an allied hard-line organization with a history of violence, enjoy significant influence.
In an ominous sign of what's ahead, suspected militants killed 25 policemen in Sinai on Monday in a dramatic escalation of the unrest roiling the strategic region, where security forces have been coming under daily attacks by Islamists since Morsi's ouster.
Other scenarios floated by insiders include the rise of a reformist Brotherhood leadership that is able to convince authorities that it represents a genuine change, as well as fragmentation into small groups or the breakaway of sizable factions to join moderate Islamist parties.
Brotherhood member Islam Tawfiq said he was confident of the group's future because the harsher the crackdown, the stronger it becomes. The 27-year-old said he was constantly on the run, sleeping somewhere different each night to escape arrest and taking part in demonstrations. He has lost more than 20 friends and acquaintances in the crackdown, he said, but remains unperturbed.
"The more killings, the more foolish actions by those behind the coup, means more pressure on the military and more strength for us," he said.