Morsi’s government unravelled late on Wednesday after the army gave him a 48-hour ultimatum in the wake of massive demonstrations since June 30 against his turbulent rule.
Military chief General Abdel Fattah al-Sisi announced Morsi’s overthrow, citing his inability to end a deepening political crisis, as dozens of armoured personnel carriers streamed onto Cairo’s streets.
And on Thursday, the army turned the screws on the Brotherhood, with military police arresting supreme leader Mohammed Badie “for inciting the killing of protesters”, a security official told AFP.
A judicial source said the prosecution would on Monday begin questioning members of the group, including Morsi, for “insulting the judiciary” as the charges began to pile up.
Other Brotherhood leaders would be questioned on the same charges, including the head of the group’s political arm Saad al-Katatni, Mohammed al-Beltagui, Gamal Gibril and Taher Abdel Mohsen.
As the world debated whether the military’s action amounted to a real coup, analysts agreed that Morsi and his Islamist movement brought about their own rapid demise.
“Morsi and the Brotherhood made almost every conceivable mistake… they alienated potential allies, ignored rising discontent, (and) focused more on consolidating their rule than on using what tools they did have,” Nathan Brown wrote on the New Republican website.
A senior military officer said the army was “preventively” holding Morsi and that he might face formal charges linked to his prison escape during the revolt that overthrew dictator Hosni Mubarak in 2011.
Morsi had issued a defiant call for supporters to protect his elected “legitimacy”, in a recorded speech hours after the military announced his ouster.
“We had to confront it at some point, this threatening rhetoric,” the officer said. “He succeeded in creating enmity between Egyptians.”
Morsi’s rule was marked by a spiralling economic crisis, shortages of fuel and often deadly opposition protests.
Thousands of protesters dispersed after celebrating wildly through the night at the news of his downfall.
“And the people’s revolution was victorious,” read the front page of state-owned Al-Akhbar.
Morsi’s opponents had accused him of failing the 2011 revolution by concentrating power in the hands of his Brotherhood.
His supporters say he inherited many problems from a corrupt regime, and that he should have been allowed to complete his term, which had been due to run until 2016.
US President Barack Obama said he was “deeply concerned” over Morsi’s ouster and urged the army to refrain from “arbitrary arrests”.
In May, Washington approved $1.3 billion in military aid to Egypt. That was now under review, said Obama, as he called for a swift return to democratic rule.
Germany termed Morsi’s ouster by the military “a major setback for democracy in Egypt”, while Russia called on all Egyptian political forces to “exercise restraint”.
Britain said it will work with the interim authorities despite not supporting the military intervention.
UN chief Ban Ki-moon said civilian rule “should be resumed as soon as possible” and that Egypt’s future should reflect the people’s will, in a statement echoed by NATO.
At least 10 people were killed in clashes in Alexandria and in the southern province of Minya during the night, security officials said.
Already in the week leading up to Morsi’s downfall, at least 50 people died in clashes between his supporters and opponents.
In addition to rounding up Brotherhood members, the security forces also turned off broadcasts by the group’s television channel, a Morsi aide told AFP.