Clearly the old leaders Washington relied on to enforce its will, like President Hosni Mubarak of Egypt, are gone or at least eclipsed. But otherwise confusion reigns in terms of knowing how to deal with this new paradigm, one that could well create societies infused with religious ideology that Americans find difficult to accept. The new reality could be a weaker Iran, but a far more religiously conservative Middle East that is less beholden to the United States.

Already, Islamists have been empowered in Egypt, Libya and Tunisia, while Syria’s opposition is being led by Sunni insurgents, including a growing number identified as jihadists, some identified as sympathizing with Al Qaeda. Qatar, which hosts a major United States military base, also helps finance Islamists all around the region.

In Egypt, President Mohamed Morsi resigned as a member of the Muslim Brotherhood only when he became head of state, but he still remains closely linked with the movement. Turkey, the model for many of them, has kept strong relations with Washington while diminishing the authority of generals who were longstanding American allies.

“The United States is part of a landscape that has shifted so dramatically,” said Mr. Malley of the International Crisis Group. “It is caught between the displacement of the old moderate-radical divide by one that is defined by confessional and sectarian loyalty.”

The emerging Sunni axis has put not only Shiites at a disadvantage, but also the old school leaders who once allied themselves with Washington.

The old guard members in the Palestinian Authority are struggling to remain relevant at a time when their failed 20-year quest to end the Israeli occupation of Palestinian lands makes them seem both anachronistic and obsolete.

“Hamas has always argued that it is the future of the changes in the region because of its revolutionary nature, that it is part of the religious political groups who have been winning the revolutions,” said Ghassan Khatib, an official at Birzeit University and former government spokesman.