The upheaval in Egypt would be a dilemma for any American administration. But the policies President Obama has followed over the past two years have made his task more challenging in three ways.

The signature policy of Obama’s predecessor, Pres. George W. Bush, was the “Freedom Agenda.” It was, in my view, flawed in both conception and implementation (a bit more on that in a moment) but the fact is that Bush did push for democratic reforms around the world — including Egypt — and that did contribute to the Cedar Revolution in Lebanon in 2005, as well as Georgia’s Rose Revolution in 2003, Ukraine’s Orange Revolution in 2004, and, of course, the Purple Revolution of Iraq in 2005 (perhaps, too, the Green Revolution in Iran, which began in 2009 and may not be entirely extinguished yet).

If the Obama administration had maintained that policy, the Lotus Revolution in Egypt — and the Jasmine Revolution that immediately preceded it in Tunisia — might have been seen as waves in an American-generated tide.

Instead, Obama rejected Bush’s policy. He took the view, shared by most European leaders, that in such regions as the Middle East, stability trumps liberty. As a result, those marching in the streets now do not view Obama as a proponent of hope and change.

Second: Less than two years ago, President Obama chose Cairo as the venue for his pivotal speech to the Arab and Muslim worlds. That sent the message that he saw Egypt as the capital of those worlds. His speech was primarily an apology for America’s past sins. He did not emphatically appeal to the region’s rulers to reform. As a result, any calls he now makes in favor of reform ring hollow.

Third: When Iranians rose up against the tyrannical regime that has ruled them for more than 30 years — when they marched in the streets chanting, “Obama, are you with us or against us?” — the president mostly held his tongue, reluctant to jeopardize his policy of “outreach” to Iran’s rulers. Can Obama now be more supportive of Egyptians as they confront a regime that, while authoritarian, is nowhere near as oppressive and brutal as that in Tehran?

Everything above is grist for the historian’s mill. For policymakers, the question that matters is this: What does the president of the United States do now?

The Egyptian military is Egypt’s most respected institution and the most likely to survive the current turmoil. After all these years of providing funds, equipment, and training to Egypt’s military, the Pentagon has cultivated allies — Egyptian officers who are disciplined and capable; who want to see their country become free, democratic, and prosperous; and who do not want to find themselves taking orders from mad mullahs and scowling Islamist intellectuals. They also grasp Egypt’s need for continuing U.S. military aid.

Obama ought to be empowering American officers to reach out — in confidence — to their Egyptian colleagues, urging them to take charge. Their duty is to prevent anarchy after Pres. Hosni Mubarak’s long-awaited retirement — which they should arrange to begin as soon as possible.

One officer must take the helm. He would make clear that he has no personal ambitions. His mission is simply to prepare the nation for free and fair elections. When? As soon as possible — but no sooner. Sufficient time must be allowed for new political parties to be organized as they could not while Mubarak was in power. Currently, the only well-organized opposition in Egypt is the Muslim Brotherhood, a more nefarious organization than many people understand.