Ties With Egypt Army Constrain Washington - "We need them for the Suez Canal, we need them for the peace treaty with Israel, we need them for the overflights, and we need them for the continued fight against violent extremists who are as much of a threat to Egypt’s transition to democracy as they are to American interests.”

From The New York Times:

Most nations, including many close allies of the United States, require up to a week’s notice before American warplanes are allowed to cross their territory. Not Egypt, which offers near-automatic approval for military overflights, to resupply the war effort in Afghanistan or to carry out counterterrorism operations in the Middle East, Southwest Asia or the Horn of Africa.

Losing that route could significantly increase flight times to the region.

American warships are also allowed to cut to the front of the line through the Suez Canal in times of crisis, even when oil tankers are stacked up like cars on an interstate highway at rush hour. Without Egypt’s cooperation, military missions could take days longer.

Those are some of the largely invisible ways the Egyptian military has assisted the United States as it pursues its national security interests across the region — and why the generals now in charge in Cairo are not without their own leverage in dealing with Washington in the aftermath of President Obama’s condemnation Thursday of the military’s bloody crackdown on supporters of the former president, Mohamed Morsi.

In his first overtly punitive step, Mr. Obama canceled the Bright Star military exercise, the largest and most visible sign of cooperation between the armed forces of the two nations. But given the growing violence in Egypt, it might have been impossible to guarantee the safety of the thousands of American troops scheduled to deploy for the war game, and the decision to call it off might have been the wise move regardless of the politics.

For the Pentagon, which had earlier delayed the delivery of four F-16 fighter jets to the Egyptian Air Force, other steps might be more difficult.

“We need them for the Suez Canal, we need them for the peace treaty with Israel, we need them for the overflights, and we need them for the continued fight against violent extremists who are as much of a threat to Egypt’s transition to democracy as they are to American interests,” said Gen. James N. Mattis, who retired this year as head of the military’s Central Command.

While a cozy relationship with the Egyptian military might be preferable for American interests to a radicalized, hostile government in Cairo, there is also a threshold of violence — still unknown — that, if passed, would make it impossible for the Defense Department to continue its dealings there.

As Egyptian generals familiar with the American military are no doubt aware, there have been instances when the United States restricted or even severed military-to-military relations with a useful ally, for periods both long and short, because of authoritarian practices, human rights violations or security policies at odds with those of the United States. Among the examples are Indonesia, Pakistan and the Philippines.

In the meantime, Obama administration officials are taking a hard look at possible incentives and punishments that might compel the generals in Cairo to end the crackdown and open a dialogue on transition to democratic governance.

“The violence is intolerable, but clearly they feel the nation of Egypt is facing a sovereign, existential crisis,” said one Obama administration official. “So while the violence is intolerable, we may be able to eventually accept these decisions if the violence ends, and quickly.”

The risk is that the United States may be left standing by as its allies in the Egyptian military lose control of the crisis.

For decades the Egyptians have helped the American military in ways that are largely unknown to the American public, said Robert Springborg, a professor at the Naval Postgraduate School in Monterey, Calif., and an expert on the Egyptian military. Mr. Springborg noted that in the run-up to the invasion of Iraq in 2003 — after the Turkish Parliament refused to allow the American military to use Turkish territory for crossing into Iraq from the north — Egypt gave the Pentagon immediate access for two aircraft battle groups and accompanying aircraft through the Suez Canal and across its territory.

Given the number of countries in the region that do not allow American military overflights, especially for combat missions, Egypt’s location makes it a vital, and relatively direct, access route to an unstable crescent of strategic importance.

Egypt’s role in the Camp David agreements has also been of critical value for America’s closest ally in the region, Israel. In the four decades before Camp David, Israel and Egypt fought several major wars; in the nearly four decades since, none. Even in the current crisis, the military communications systems established by Camp David to link Israel and Egypt have helped defuse tensions. When Egypt recently moved additional troops into the Sinai Peninsula — in violation of the accords — Israel quietly assented, knowing that the extra forces were to secure the border and tamp down rising militant activities.

The Obama administration has notably avoided threatening to cut off the $1.3 billion in annual military assistance to Egypt, recognizing that the money has helped guarantee peace with Israel for the past 35 years. All of the aid for this year already has been authorized, so even an order to halt the financial assistance would not have an impact until next year. In the meantime, Saudi Arabia and other oil-rich Persian Gulf nations have increased their financial support to Egypt, far surpassing the American contribution.

Beyond delaying shipment of the F-16 warplanes, officials said, there are few unfulfilled weapons contracts that could be held up as a punitive measure.

American officials looking at ways to punish the Egyptian military for the order to clear Muslim Brotherhood protest sites have looked to the lesson of Pakistan, which came under economic sanctions for its nuclear program.

Among the actions taken was ending a program of inviting young Pakistani military officers to attend armed service academic programs in the United States. One result has been a generation of Pakistani officers with no affinity for — and, more often, hostility toward — the American military. A similar result could occur if the next generation of promising Egyptian officers were not invited to American military schools.

In the end, one powerful incentive for the generals to quickly end the civil unrest and establish order — and try to make good on promises to begin a transition to legitimate governance might be economic — to attract tourism and investment. And also to preserve Egypt’s relationship with the United States.

“Both sides have a strong interest in preserving it and will work to that end,” Mr. Springborg said. “The Egyptian military will take steps to clothe the military’s behind-the-scene rule with suitable civilian trappings, making it possible for the U.S. and others to deal with it.”