Obama was appalled. “We can’t return to business as usual,” he declared after the slaughter. “We have to be very careful about being seen as aiding and abetting actions that we think run contrary to our values and ideals.”

Several weeks later, Obama halted the planned delivery of U.S. military hardware to Cairo, including attack helicopters, Harpoon missiles and several F-16 fighter jets, as well as $260 million in cash transfers. He also cast doubt on the future of America’s $1.3 billion in annual military aid to Egypt—a subsidy on which Cairo depends heavily, and much more than the United States sends to any country in the world aside from Israel.

But a fierce internal debate soon broke out over whether and how to sanction Egypt further, a fight that many officials told me was one of the most agonizing of the Obama administration’s seven years, as the president’s most powerful advisers spent months engaged in what one called “trench warfare” against each other. It was an excruciating test of how to balance American values with its cold-blooded security interests in an age of terrorism. Some of Obama’s top White House aides, including his deputy national security adviser, Ben Rhodes, and the celebrated human rights champion Samantha Power, now U.S. ambassador to the United Nations, urged the president to link further military aid to clear progress by Sisi on human rights and democracy. But Secretary of State John Kerry, then-Defense Secretary Chuck Hagel and Hagel’s successor, Ash Carter, argued for restoring the aid. Trying to punish Sisi would have little effect on his behavior, they said, while alienating a bulwark against Islamic radicalism in an imploding Middle East. “Egypt was one of the most significant policy divides between the White House and the State Department and the Department of Defense,” says Matthew Spence, a former deputy assistant secretary of defense for Middle East policy.

For months, Obama tried to split the difference. In meetings and phone calls with the Egyptian ruler, by now paranoid and resentful about America’s intentions, Obama and Kerry urged Sisi to respect human rights, while also seeking his help in countering the the metastisizing Islamic State in nearby Syria and Iraq. Sisi did little of either.

In the end, Obama folded.