Thankfully it appears there was a bloodless coup in Egypt (although the situation is fluid) with Morsi under military house arrest, which means the Muslim Brotherhood is out of power. The Obama administration is predictably flip-flopping all over the place in trying to wedge themselves onto the winning side, perhaps even pretending the coup we all saw wasn't really a coup (because of this).
But what about al Qaeda? It's now being run by an Egyptian, Ayman Zawahiri, whose brother Mohammed was released from prison by the Morsi government (along with other Islamic militants). Mohammed was instrumental in starting the initial Cairo riots on 9/11 (designed to get the Blind Sheikh released) while reports out of Libya are saying that several Ansar al-Sharia members under arrest have pointed a finger of blame at Morsi in the Benghazi attack. Most legacy AQ terrorists, such as Zawahiri, bin Laden, and KSM, got their radical starts with membership in the Brotherhood.
Zawahiri's dream was to hold an actual state government in Arabia from whence he could begin the worldwide caliphate. In other words, he's going to be pissed about these recent developments. And a pissed off AQ has historically been a bad thing. Good thing the GWoT is pretty much over.