The military proved disastrously inept when it tried to govern Egypt after the overthrow of Hosni Mubarak in 2011. Now, a week after ousting Mohamed Morsi, the first freely elected president, the military is orchestrating an even more dangerous maneuver. We are deeply fearful that Egypt could devolve into civil war, which would add new trauma to a region already in turmoil.

On Wednesday, the general prosecutor’s office issued formal arrest warrants for some of Mr. Morsi’s political allies in the Muslim Brotherhood — the top spiritual leader and at least nine other senior figures — who were accused of inciting the deadly protests that occurred on Monday. That is an outrageous move given that at least 51 protesters were killed by soldiers and police officers, and hundreds more wounded, most of them unarmed as they demanded Mr. Morsi’s release from detention and his reinstatement as president.

On Wednesday, Amnesty International said it had evidence showing that security forces used excessive force against Mr. Morsi’s supporters. Gunning down Morsi supporters and attacking an entire group could destroy hope for the democratic process and could well push the Brotherhood into violent extremism.

There are also plenty of reasons to be alarmed about the military’s plan, put forward on Tuesday, to transition from a military-appointed interim civilian government to an elected one. The “constitutional declaration” issued by Adli Mansour, the newly installed president, made clear that the government’s authority comes only from the top commander, Gen. Abdul-Fattah el-Sisi.