Egypt’s shift into the greater uncertainties of the post-Mubarak era has great consequences for Centcom, as well as for the long-simmering Israeli-Palestinian conflict, in which Mubarak was always a key ally for both the United States and Israel.

In the short term, it is likely that little will change in Egypt’s relationship to Centcom. After all, the vacuum left by Mubarak’s departure has for now been filled by a shadowy body called the Higher Council of the Egyptian Armed Forces (HCEAF), which is led by Defense Minister Mohamed Sayed Tantawi. However, the generals who run the HCEAF understand that, if they are to avoid a replay of the open confrontations that Egypt’s cities saw over the past three weeks, they urgently need to reach a power-sharing agreement with the country’s political forces that will lead to a much more accountable, democratic, and inclusive form of civilian rule.

During the past three weeks, the generals – and all Egyptians – came to understand two key things. First, in the modern era there is no way the military can use brute force to suppress a massive popular uprising without that tactic backfiring badly. And second, any prolonged confrontation in the streets can have economic consequences that harm everyone. (Egypt’s military as a body, and numerous recently retired generals as individuals, all have large economic enterprises that were badly dented when Mubarak briefly shut down the internet, and therefore all normal banking and commerce in the country.)

So Tantawi and his HCEAF colleagues are already negotiating. The important negotiations are those with three different groups from the former opposition:The younger, mainly secular, protesters from the April 6 Youth Movement and its allies; the more ‘establishment’ secular politicians from the so-called "Wise Men" group; and the coalition led by Egypt’s powerful and well-organized Muslim Brotherhood (MB).

Events have been moving so quickly that it is hard to say what the programs of these three groups – or, indeed, of the Egyptian military themselves – will be on the issues of concern to U.S. planners. Until now, all those Egyptian actors were focused almost solely on the issue of Mubarak: whether he would stay in power, or leave. And for the weeks ahead, they will have to focus most of their energy on working out the details of their own internal transition, including deep constitutional changes, reaching agreement on new electoral laws and political freedoms, and the holding of truly democratic elections.

In the course of this transition, these Egyptian parties and forces will also be working out the basis of their new relationship with Washington.  

The generals themselves will want to keep the ties as tight as possible. They receive the bulk of the aid that Washington has been giving to Egypt: $1.3 billion a year, and I suspect they will want to keep as much of that aid coming as possible!

The opposition movements are wary of the United States and deeply critical of many U.S. policies – especially on the crucial (for most of them) Palestine Question. But most of them, including the MB, want Egypt to keep on good terms with America. Indeed, they are probably far warier of their own military than they are of Washington!  

The Obama administration therefore has some opportunity to use its close ties with the Egyptian military and the ties it now needs to build with all the strands of the opposition, to help support all these actors as build a new, more democratic order. If it does this, our country can be seen as a valued friend of the emerging democratic Egypt, and this will be a great investment for many years to come.

Several aspects of U.S. policy may, however, threaten this outcome. One key one is that Pres. Obama does not have any high-level advisers who understand enough about Egypt and the rest of the Middle East to give him steady information and advice. Thus far he and Secretary of State Hillary Rodham Clinton have relied far too heavily on Israel-centered advisers who understand little about the internal dynamics of Arab countries, having always until now relied only the relationships with key local autocrats. That lack of good advice led to policies that were, and were seen as, embarrassingly unsteady.

Now, Obama and Clinton need to bring in a new cohort of senior advisers who speak Arabic, who understand the whole region, and who do not view it only through Israel-centered eyes.

Another threat to Washington’s ability to deal with democracy emerging in Egypt, Tunisia, and other Arab countries is the drumbeat of Islamophobia that is a rising presence in much of America, including in some portions of the U.S Congress.  

American Islamophobes are people who denigrate all or most Muslims and refuse to recognize that even within the realm of “political” Islam there is a world of difference between, for example, the moderately Islamist “AK” Party that’s been ruling Turkey for nine years (and has kept Turkey as a valued NATO ally), and the violent, misogynistic extremists of Al-Qaeda or the Taliban.

Egypt’s MB is much, much closer to Turkey’s AK Party than it is to the Taliban, and its leaders have gone out of their way to say they want good relations with the United States. They have been strictly nonviolent for many decades. They are also an organized force inside Egypt that cannot be excluded from any new democratic order. If the Obama administration works to exclude or marginalize the MB from influence in Egypt’s new democracy, and to play favorites within in, this could backfire badly.

So the Obama administration has a lot to do as it figures out how to react to last week’s events in Egypt. But given how inspiring those events were, this challenge is a fine one to have!

Helena Cobban, a veteran Middle East analyst, blogs at Just World News.