Wednesday’s clashes between the Egyptian military and pro-Muslim Brotherhood protestors were predictable and, at the cost of over five hundred lives, tragic. And with the Brotherhood calling for more marches and demonstrations, the violence may worsen before it begins to decrease.

Western leaders are now scrambling to try to halt the killing and create some form of political reconciliation. The United States has the most important role, as the patron-in-chief of the Egyptian armed forces, must play the leading role in this political drama. On Thursday morning, President Obama decried the actions of Egypt’s interim government since the coup-that-wasn’t as well as yesterday’s bloodshed, which included violence by protestors, by the military, and against churches. He insisted that Egypt should commit to a path of nonviolence and democracy and cancelled upcoming joint U.S.-Egyptian military exercises.

In the end, it is difficult for statesmen—even the most idealistic—to resist the overwhelming incentives to make decisions on the basis of core national interests above second-order interests such as the spread of democracy and human rights. This is not a criticism, but rather a recognition that while the streets of Cairo have been restive, America’s core interests in the Middle East and North Africa have remained stable. These interests are commonly understood as access and trade through the Suez Canal and maintaining peace between Israel and its Arab neighbors and, consequently, stability in the Mediterranean littoral.

As such, President Obama’s administration was careful to orchestrate Mubarak’s stable departure and has since sought to maintain friendly relations with whoever might be in charge in Cairo. When the Supreme Council of the Armed Forces overthrew Mohamed Morsi, President Obama was—and remains--reluctant to brand the event a “coup,” as that would trigger a legally mandated end to sizeable U.S. military aid that is thought to keep the peace between Israel and Egypt. Even after Wednesday’s massacre, he still labeled it an “intervention.”

But the White House appears to understand that core American interests do not stop at the Suez and peace with Israel. The administration has been pushing for political reconciliation between Egypt’s various factions—namely the Egyptian military, the Muslim Brotherhood, and the fissiparous liberals (there are other factions, of course, but, counterintuitively, the most extreme of them—the Salafis—are easier to manage, at least for now). Not only does such a reconciliation remain possible after this week’s bloodshed, but it also is even more imperative.

Reconciliation may not be possible right now, but it is the only approach that can end the cycle of extralegal competition between Egypt’s Islamists and military that has had such deleterious consequences for the region and the West. These consequences have included political upheaval and the growth of an extremism greater than that espoused by the Muslim Brotherhood: the global militancy of Al Qaeda, which can be traced in many ways directly to Egypt’s prison cells.

A ruler was toppled, the Muslim Brotherhood responded to opening political systems, over-reached, and the system closed down on them. This is not the first time they have been down this road.

In 1951, the Anglo-Egyptian Treaty was declared void by a newly elected Wafd government. This created a crisis, and the Muslim Brotherhood led calls for jihad against the British. They sent a force of three hundred armed volunteers into the Canal Zone where they attacked British military positions. The government’s inability to resolve the crisis led to widespread disorder throughout Egypt. The heart of Cairo, the most Westernized part of the city, was burned to the ground on January 26, 1952. Martial law was declared, and the leadership of the Brotherhood was briefly detained. What followed was a complex serious of events and violent episodes that culminated in July with the Free Officers Revolution, a military coup. The Free Officers, with the cooperation of the Muslim Brotherhood, seized control of Cairo and the country, toppling the monarchy.

By 1954, Gamal Abdel Nasser, one of the Free Officers, had consolidated control over the revolution. In the same year, the Brotherhood was dissolved and repressed to such a degree that Richard Mitchell, author of the definitive early history of the movement, predicted it would never rise again. The immediate cause was a purported attempt on Nasser’s life. The Brothers were arrested by the thousands and imprisoned, some without trial. A few of its leaders escaped the country. Brotherhood cadres sat scattered in various prisons across the country.

Eleven years after the 1954 crackdown, the brutal imprisonment and elimination of Organization 1965—a militant Brotherhood faction that looked to Sayyid Qutb for leadership and vision—did little to change anyone’s mind about the Brotherhood’s lack of a future. Organization 1965 was a violent revolutionary cell within the broader movement that did not engage in licit politics. It wanted war. And it was crushed mercilessly.

The Brotherhood’s failure to achieve political power drove elements of the movement, which had been hardened in the prisons of Egypt and elsewhere, to seek more drastic means. This failure, combined with Sayyid Qutb’s electrifying influence, the demonstrative effect of the Iranian revolution, and the cauldron of the Soviet-Afghan War led to the conviction among some Islamists that there was no longer any point in working inside the system to change it. Violence made more sense. Indeed, the adoption of violence by a political group is a strategic choice that is usually only made once activists believe other means have been exhausted.

Ayman al-Zawahiri, the current head of Al Qaeda, explained in his opus, Knights Under the Prophet’s Banner:

The jihad movement in Egypt began its current march against the government in the mid-1960s when the Nasirite regime began its famous campaign against the Muslim Brotherhood group in 1965….The authorities thought that they had eradicated the Islamic movement in Egypt once and for all. But God willed that those events were the spark that ignited the jihad movement in Egypt against the government.

Thus began the division of the Islamist movement into two conceptual tendencies, one which seeks to Islamicize society through activism, preaching and political competition, and the other, which later came to be represented by al-Zawahiri’s Al Jihad and Al Qaeda, that believes only violence can bring about the necessary change. Mohammad Qutb, Sayyid’s brother, was one of Osama Bin Laden’s university instructors in Saudi Arabia, where he fled. The rest is well-worn history. Not only did the Brotherhood flourish once again, but so did violent jihadists. And the Middle East’s political feuds came to New York and Washington in September 2001 to terrifying effect. The United States cannot allow this history to repeat itself or even, as Mark Twain phrased it, rhyme.

To maintain stability and American patronage, the Egyptian armed forces must show to the world that the most populous Arab state can incorporate Islamists without bloodshed or repression if they too denounce violence and factional supremacism. And the Muslim Brotherhood, if given another opportunity to take part in governance, must show that it can govern without resorting to the majoritarian and exclusionary tendencies that crippled its legitimacy over the last two years, or it risks facing a repetition of the repression it suffered under Nasser.

How can the United States leverage its influence in Egypt toward reconciliation? On Thursday morning, President Obama announced the cancellation of upcoming joint U.S.-Egyptian military exercises. That was a good start. However, the White House and the Congress should resist turning America’s military aid to Egypt, totalling over $1 billion, into a bargaining chip. This aid purchases an Egyptian foreign policy free of belligerence toward Israel. This is not to say Egypt would inevitably go to war if aid were to be cut. But the aid does underwrite and incentivize cooperation between Egypt and Israel that might not otherwise be defensible in the face of antipathy towards Israel that pervades all levels of Egyptian society. An American attempt to tie military aid to Egypt’s domestic political order risks upending the security architecture in the Eastern Mediterranean.

The United States can use other ways and means to build an incentive structure that rewards the Egyptian military for desired behavior and penalizes them for short-sighted crackdowns. To build this structure, it is crucial to understand what all parties—and the military in particular—want. For example, America should not hesitate to threaten block a $4.8 billion loan from the International Monetary Fund, which almost all of Egypt desperately craves, if the military continues to slip back into a Mubarak-style autocracy. On the positive side, if the Egyptian military turns back in the right direction, Washington can offer to provide far more intelligence and material support to the Egyptian military’s ineffective operations against militancy, smuggling and banditry on the strategically significant Sinai Peninsula. The United States can also offer to deploy its diplomatic and economic clout to discourage Ethiopia’s plans to dam the Nile and thereby deliver a blow to Egyptian water security. The time to offer such support in exchange for steps toward reconciliation is now, as Egyptian officials are expected to meet with their Ethiopian and Sudanese counterparts by the end of August.