Commanders of Syria's Western-backed opposition fighters met Thursday to try to salvage their efforts to oust Bashar al-Assad's regime after Islamist rebels ran them out of their headquarters, threatening to sideline the steadily weakening group.

The takeover of Gen. Salim Idris's facilities by Islamist fighters over the weekend caught the Obama administration by surprise and threw U.S. policy into turmoil. Officials said they were struggling to piece together what happened and what it meant for support of the moderates....