U.S. Defense Secretary Leon Panetta, center, meets with newly elected Egyptian President Mohamed Morsi, right, and the leader of Egypt's military, Field Marshal Mohammed Hussein Tantawi, in Cairo July 31, 2012. (AP Photo)

Egyptian President Mohamed Morsi is scheduled to arrive in New York tomorrow, September 23, to attend the United Nations General Assembly meeting. This will be his first visit to the United States as president of Egypt. It is something of a momentous occasion, particularly in light of the riots at the U.S. embassy in Cairo last week. While Morsi will not meet with President Obama during this visit, the fact that he did not cancel the trip is an indication of how little the events of last week actually shook the core of U.S.-Egypt relations.

Understanding the beating heart of relations between the two countries requires some deep digging. The State Department has announced on its website that, “Supporting a successful transition to democracy and economic stability in Egypt, one that protects the basic rights of its citizens and fulfills the aspirations of the Egyptian people, will continue to be a core objective of U.S. policy toward Egypt.”

That security and economic cooperation are at the heart of U.S-Egypt relations is unsurprising. It bears repeating, however, on the occasion of the President’s visit because in many ways, Morsi represents only a sliver of the complex relationship between the two countries. Morsi’s election to the presidency was undoubtedly historic and many have great optimism about his abilities to improve Egypt’s domestic situation and reinvigorate Egyptian leadership in the region. The fact, though, remains that in the broad scope of U.S. relations with Egypt, the President is a sideshow.

It is the military to military relationship of the past 30 years that truly defines the core of U.S.-Egypt relations. It is not merely an institutional relationship, but rather, one between individuals who have trained together throughout this period. The general who replaced Field Marshall Tantawi in August as the new Minister of Defense and Head of Military Intelligence is one such individual. General Abdul Fattah El Sissi first participated in infantry training at Fort Benning, Georgia in 1981.

In reporting on Gen. El Sissi’s appointment, the Wall Street Journal noted that Tantawi’s forced retirement may not have significantly altered the balance of power between Egypt’s military and the civilian government. Rather, “Mr. Morsi faces huge challenges if he hopes to truly unravel the military from the Egyptian state, a process that analysts and observers say could take generations. The military enjoys profound public loyalty, an expansive commercial empire, and the support of a judicial system that has repeatedly ruled in its favor.”

While the military is certainly challenged regularly by activists in Egypt, on the occasion of Morsi’s visit to the United States, it is important to remember that the “transition” to civilian rule and democracy is not inevitable in Egypt or elsewhere in the world. In terms of U.S. policy toward Egypt, there is no question that the United States would prefer to work with a government that was accountable to its citizens, maintained the rule of law, and protected human rights.

But, when push comes to shove, democracy is not the bottom line for the United States. For example, when Egypt’s highest court dissolved the elected parliament and when the military issued a constitutional declaration awarding itself legislative powers, the United States did not withdraw its aid to Egypt. Even when the Egyptian government arrested the employees of American NGOs and after the recent riots outside the U.S. embassy, reforms to U.S. aid and to the relationship in general were not really under consideration.

Egypt has been the third largest recipient of U.S. military aid for the last 60 years. This legacy has proven to be a major obstacle to democratic reforms within Egypt’s government. While Morsi’s election is a major departure from decades of military rule in the country, the United States also has a critical role to play in reforming its relationship to the Egyptian military in order for civilian government to hold sway in the country.