Some in the administration and Congress will try to avoid this step, because of the armed forces’ history as a U.S. ally and guarantor of peace with Israel. But the suspension of aid is the necessary first step in a U.S. policy that advances the aim Mr. Obama laid out in a Wednesday night statement: “to ensure the lasting restoration of Egypt’s democracy.”…

The Obama administration should now make clear to the new military-backed regime that aid will be restored only if a genuinely democratic transition is pursued in the coming months. That means tolerance for all peaceful political forces, including the Muslim Brotherhood — whose leaders, including Mr. Morsi, should be immediately released. It means acceptance of free assembly and free media, including the Islamist broadcasters that have been shut down. Any changes to the constitution should be the result of a consensus among all political forces, without diktats by the military. And there must be a firm — and short — timetable for new parliamentary and presidential elections.

Had the armed forces not intervened, democracy probably would have led to the defeat within months of the Muslim Brotherhood in legislative elections. If it does not provoke the eruption of violent conflict, this coup may well ensure that Islamist forces, including more radical groups, grow stronger. The United States must focus on preventing the worst outcomes in a vital Arab ally, including civil war or a new dictatorship. That means dropping its passivity and using the leverage of aid to insist on a democratic transition.