In the broad range of the political Islam movement - from moderates to militants - the Brotherhood eventually emerged as the central force arguing that Islamists can be democrats. Their influence drew in harder-line groups to participate at the ballot box. Ultraconservatives who once refused elections that could potentially bring any law but God's law took their chance at the polls.
In an impassioned Facebook post just before the army pushed Morsi out Wednesday, one of his top advisers Essam el-Haddad argued that what was happening was irrevocably damaging democracy itself, saying the Brotherhood had been unfairly treated. He insisted history would show the Brotherhood tried to include others in its administration but was shunned.
"Increasingly, the so-called liberals of Egypt escalated a rhetoric inviting the military to become the custodians of government in Egypt," he wrote. "The opposition has steadfastly declined every option that entails a return to the ballot box."
But amid multiple complaints, opponents point to a key factor that turned many against the Brotherhood: the post-Mubarak constitution. Morsi had vowed a consensus on the landmark document, but Islamists dominated the panel writing it. Liberals, leftists, secular politicians and Christians steadily dropped out, complaining Morsi's allies were forcing their vision. In the end, Morsi unilaterally decreed himself and the assembly untouchable by the courts to ensure judges did not dissolve the panel, while Islamists hastily finished writing the charter in an all-night marathon session.
It was rushed to a referendum, where it passed with a hearty 63 percent of the vote - but only just over 32 percent of the electorate casting ballots.
Meanwhile, Brotherhood members and other Islamists were steadily were given more posts across the government, fueling a perception that they were taking over institutions - though they constantly faced resistance on many fronts from the entrenched bureaucracy. Islamist rhetoric from officials and clerics on TV rang in the ears of many as divisive and harsh.
Morsi's ouster could now send the Brotherhood into disarray for years to come, just as a major crackdown on the group did in 1954. Morsi and many of his advisers have been put under house arrest, and he could face trial for escaping prison during the 2011 uprising. Two top leaders of the group, including the head of its political party Saad el-Katatni, were arrested and at least 30 more were expected to meet the same fate.
The danger now could be that a heavy crackdown will turn into forcibly excluding them from politics once more. The Brotherhood was banned for much of its 83-year existence. But it still maintains a powerful, organized and disciplined network of members nationwide.
"The forceful removal of the nation's first democratically-elected civilian president risks sending a message to Islamists that they have no place in the political order; sowing fears among them that they will suffer yet another bloody crackdown; and thus potentially prompting violent, even desperate resistance by Morsi's followers," the Brussels based International Crisis group warned in a statement.
