The Obama administration was said to have favored the Arab Spring movement which led to the overthrow of dictator Hosni Mubarak in Egypt in 2011, among other things. In the first democratic election in Egypt's history Dr. Mohamed Morsi's Freedom and Justice Party won a solid majority in Egypt's parliament. Several months later General Abdul Fatah al-Sisi overthrew the elected parliament and Dr. Morsi, who had received his PhD in electrical conductivity from the University of Southern California was arrested, and still remains in prison. https://en.wikipedia.org/wiki/Mohamed_Morsi US CENTCOM (Central Command in the Mid-East) probably aided and abetted the military coup, but in any case the Egyptian generals continued to receive millions of dollars in US military aid during the coup and still get millions. This seems very similar to Operation Ajax in Iran in 1953 in which the CIA and British MI 6 overthrew the only democratic Muslim government in the Mid-East of Dr. Mohammed Mossadegh. Some powers in the US apparently wanted to restore a pro-US dictatorship in Egypt. Call them the secret police, "the intelligence community," the Deep State or simply the establishment, but it was not the US Commander-in-Chief and his administration. The establishment's disinformation campaign is in full swing now, and it is questionable whether Trump will be able to promote détente with Russia even if he can get Congress to go along with him.
