“Mission Accomplished” read the hauntingly familiar phrase from Egyptian activist Wael Ghonim on Thursday when the first word came that President Hosni Mubarak might step down. Ghonim delivered the words by Twitter, unlike George W. Bush, who had them printed on a banner. But in both cases, they were premature.

As Richard Haas, a former top State Department official who now heads the private Council on Foreign Relations, said in a conference call last week, if Egypt’s revolution were a baseball game, this would only be the third inning.

That’s not to diminish the success of the protesters who filled Tahrir Square for 18 consecutive days before Mubarak resigned. But the president’s resignation was really just a necessary prologue to the real mission: establishing democracy.

That goal still faces many obstacles. For starters, even with Mubarak gone, most of his generals still are there. Egypt’s military has supplied the country’s leaders for almost 60 years, since the revolution of 1952. Mubarak, 82 and ailing, was on his way out already, and some members of the Supreme Council — beginning with his right-hand man, Gen. (and now Vice President) Omar Suleiman, already had their eyes on the president’s job. Suleiman has scoffed openly at the idea that Egypt is “ready for democracy.”

The country’s military elite is not populated by civil libertarians; the journalists and human rights activists who were arrested in Tahrir Square last week were imprisoned by Suleiman’s military intelligence units.

Left to their own devices, it’s unlikely the generals, though they’ve promised constitutional changes, an end to the repressive state of emergency and new elections, will push for a swift transition to a full and free democracy.

Mohamed ElBaradei, the former chief of the U.N. International Atomic Energy Agency who has offered himself as a transitional leader, has proposed a three-man “presidential council” with only one of the seats reserved for the military. He also is calling for the drafting of a wholly new constitution and elections within a year.

But Egypt’s next step is far from certain.

The inevitable messiness of the ensuing process will present hard choices for the Obama administration too. President Obama said last week that he hoped Egypt’s democratization would be both “orderly and genuine.”

He must know that those two goals, while not contradictory, are in tension. The administration wants more from Egypt than just democracy; it also wants to maintain Egypt’s stability, its close military relationship with the U.S. and its peace with Israel. That’s why the word U.S. officials used most often over the last 18 days was “orderly,” and why Obama felt it necessary to add the democracy-friendly modifier “genuine.”

The administration is understandably concerned that Egypt’s next political leaders — whether they turn out to be the Supreme Council of the Armed Forces, the Facebook insurgents in Tahrir Square or even the Muslim Brotherhood — won’t be as strongly pro-U.S. as Mubarak was.

“They must know that they will continue to have a friend in the United States of America,” Obama said. But after more than 30 years of support for the military governments of Mubarak and his predecessor, Anwar Sadat, it might prove difficult to convince Egypt’s democrats that the United States was on their side all along.

Obama made a start on that process when he praised Egypt’s military for its role as “caretaker to the state” but pointedly defined its mission now as guaranteeing a real transition. “Nothing less than genuine democracy will carry the day,” he said.

And, he added, the United States will help. “We stand ready to provide whatever assistance is necessary,” he said.

But that was a promise that might be difficult to keep. The new Republican majority in the House already has proposed deep cuts in foreign aid, including the programs that would help Egyptian democracy. Sen. Rand Paul, R-Ky., the leader of the Senate’s new “tea party” caucus, has proposed eliminating foreign aid entirely, including for Egypt and Israel. Others would cut Egypt but spare Israel, a move that wouldn’t make the U.S. popular in Tahrir Square.

Some of those same House Republicans pressed the State Department last week to bar the Muslim Brotherhood from playing any role in a new Egyptian government. They didn’t explain how to do that while reducing U.S. aid — and thus U.S. leverage — at the same time.

The insurgencies in Egypt and Tunisia have presented the United States with an extraordinary opportunity: a chance to nudge, advise and aid countries that are moving toward democracy in the world’s most dangerous region. Taking advantage of that opening, which leaders of both U.S. political parties have sought for decades, will require money, energy and patience. It’s a pity that such an opportunity has arrived when we seem to be short of all three.

Doyle McManus is a columnist for the Los Angeles Times.