Egypt's Muslim Brotherhood Now

Mostafa Hashem describes shifts in the Muslim  Brotherhood organization under Sisi:

After about a year of internal conflicts, the Muslim Brotherhood in Egypt has finally begun a comprehensive restructuring process. For the first time, the group is empowering its youth to lead the organization. This shift in approach reflects the former leadership’s realization that it has failed to adapt to domestic politics and Abdel Fattah el-Sisi’s crackdown since the ouster of Mohamed Morsi in July 2013.

The Muslim Brotherhood, in response to the crackdown, has conceded to the will of active youth members and others who support an escalation with the Sisi government. The shift came after Brotherhood youth finally refused to work with the group’s secretary-general, Mahmoud Hussein, who had sidelined them during Morsi’s administration...The Muslim Brotherhood’s old guard worried that a major loss of youth supporters would sink the Muslim Brotherhood as both an ideology and an organization.

In response to these difficult circumstances and increasing pressure from the youth, the group’s leadership has restructured the organization based on internal elections that lasted two months—as they took place not just in Egypt but also Qatar, Turkey, Malaysia, and Sudan—and ended at the beginning of January. The most important changes to date were a shift toward decentralization, a focus on preaching and charity work, and the election of a new “committee to manage crisis and mobilization." 

This is in contrast with the organization under Nasser, where the prison leadership under Hassan al-Hudaybi kept control of the organization and worked to limit the influence of its more confrontational elements, as represented by Sayyid Qutb.  Two things are different this time.  One is the fact that the Muslim Brotherhood came to power democratically, but was overthrown.  This fulfulled the "Algeria paradigm," in which many Islamists believed other powers in society would not allow them to rule even if they came to power through a fair process.  The fact the Muslim Brotherhood in power acted in a high-handed majoritarian manner, taking their narrow election win as a mandate to implement a broadly Islamist agenda, does not factor into this.

This second factor, is the article mentions this, is the rise of Islamic State.  Although its ideology is much more radical than the Muslim Brotherhood has historically been, the fact it has succeeded in establishing a state through force of arms does make the military option more attractive to Islamists in general.  As the Muslim Brotherhood embraces confrontation in the wake of the 2013 coup, we can unfortunately expect consistent low-level MB violence in Egypt for the foreseeable future.