In what i suspected, the Muslim Brotherhood seems to have made a deal with the Military Council to share power. The Military Council seems to be backing the Muslim Brotherhood in the parliament but on the condition it supports the military council in the Presidential elections. This is my theory anyways.Muslim Brotherhood Takes 47% of Seats in Inaugural Post-Mubarak Parliament
Islamists will dominate Egypt’s first parliament following the ouster of Hosni Mubarak almost a year ago as the country prepares for the anniversary of the protests that ended his three-decade rule.
BloombergThe military council said it would cede power when a president is elected in a national vote by the end of June. In comments published by Mena on Jan. 17, Tantawi said Egypt is facing “grave and unprecedented dangers” and urged Egyptians to be vigilant to thwart “plots and conspiracies” being woven for their country.
Evidence for the Muslim Brotherhood working with the State Security comes from now under arrest former minister of interior Habib El-Adly:
sourceEssam El-Batawi, defence lawyer for former interior minister Habib El-Adly, continued laying out his case for his client’s innocence on Tuesday, claiming that Egypt’s Muslim Brotherhood (MB) had planned in advance to participate in last year’s 28 January “Friday of Rage” demonstrations in Cairo’s Tahrir Square in coordination with the interior ministry, with the understanding that protests would remain peaceful in nature.
According to El-Batawi, meetings were held between Brotherhood members and representatives of the State Security apparatus in the run-up to 28 January.
Interestingly, the military council "will release 1,959 prisoners convicted by military courts after the Jan. 25 uprising" and marks one of the only good deeds the Military Council has done so far. Also, it would be unsurprising if spies and agents of other nations, who no doubt tried to influence the uprisings, are part of those prisoners. However, there are some who aren't falling for it:
The Military is attempting to appease the critics by "partially lifting" the emergency law; whatever that means:“This is the classic pre-demonstration concession, or in this case an attempt at portraying something as a concession,” said Heba Morayef, an Egypt researcher for Human Rights Watch. Despite the moves, “the military’s whole intention is to give themselves power over the judiciary,” she said.sourceEgypt’s ruling general announced the partial lifting of a more-than-three-decades-old emergency law on Tuesday, just a day before the first anniversary of the start of Egypt’s revolt...The abolition of the emergency law, which allows the state to detain and hold Egyptians for virtually no reason, was a key demand of revolutionaries last winter, and it has remained a priority. But Tantawi reserved the right to apply the law in cases of “thuggery,” and human rights groups said the announcement would change little...“ ‘Thuggery’ is just the military’s word for Mubarak’s ‘terrorism,’ ” he said. “It is even more vague and overly broad and is used to give the police broad powers.”
It seems nothing will change, only the terms used to support indefinite detention (sounds like U.S.),
What seems obvious to me is that the control of parliament has been transferred from one party (Mubarak's) to another (MB) and does not guarantee the people any more control or influence in political matters. The political system hasn't changed in any drastic measure and therefore cannot be classified as a revolution. Instead of a secular driven country fears are that it will be Islamist. It seems that the Muslim Brotherhood will continue the strong relations with the U.S. but their relations towards Israel may suffer.
A major question is: has the Muslim Brotherhood abandoned terrorist funding? While it claims to have abandoned terrorism (it used to participate in terrorist assassinations and bombings) there is doubt that it has ceased financially assisting Sunni terrorist organizations that it had and possibly still has close connections with (HAMAS, Islamic Jihad, Al Qaeda, etc).
It seems that it still participates in terrorist activity because former head of MI6 Sir Richard Dearlove has referred to them (in 2011) as "at heart, a terrorist organisation" source.
The Council on Foreign Relations has claimed that it remains "unclear" as to whether the MB has terrorism ties. As the article notes:sourcesome of the world’s most dangerous terrorists were once Egyptian Muslim Brotherhood members, including Osama bin Laden’s top deputy Ayman al-Zawahiri.
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