Idris is "very afraid" a cornered Assad might unleash chemical weapons on the fighters. He said old friends of his still in the regime have warned him that the military, which already fired several Scuds, is training more ready-to-fire missiles on rebel strongholds in Syria's northwest.
Logistics also pose a nightmare. The 55-year-old, who studied in Germany and taught electronics at a Syrian military college, communicates by Skype with his officers. With power out most of the time, he's had important conversations cut short by a dying laptop battery, said Idris, who spoke with a professorial demeanor and wore a black suit during a brief break from the war zone.
Idris is facing resistance from some local commanders, including in the countryside near Maaret Misreen, a provincial town in the northwestern Idlib province. Some of the men, who command close-knit groups of fighters and are used to making their own decisions, dismissed Idris as a late-comer to the cause who didn't deserve to lead because he hadn't risked his life.
"We are the people who are working on the ground," Rami Bitar, 37, a former truck driver and leader of 25 men with whom he shares a two-story house. Idris "hasn't done anything yet for the country," Bitar said. "I will not accept his authority. He is coming too late."
Idris said he believes the new military command represents the vast majority of rebel fighters in Syria. At their conference this month, the field commanders chose a 260-member military council, which picked a 30-member leadership. The smaller group then chose Idris, who had spent 35 years in the Syrian military.
Observers said more than half the new leadership is believed to be Islamist, though Idris is not. "The new command is representative of where the power resides on the ground," said Joseph Holliday of the Institute for the Study of War, a Washington think tank.
The military regrouping came after Syria's fractured political opposition reorganized and won international recognition as the sole representative of the Syrian people. The West has urged anti-regime forces to unify, as a condition for stepped-up support, and suggested top rebel commanders in exile move to Syria to burnish their credibility.
Idris, who was based in Turkey after his July defection, said he took up command in the rebel-held areas on Saturday, and for much of Tuesday observed a battle between his fighters and regime forces on the outskirts of the central city of Hama.
He said he has set up five regional operations centers, staffing each with about 15 defected army officers.
Idris said he is frustrated at times with the chaos among the rebels, the vast majority of them civilians without proper military training.
"In the military, there is discipline. Here there is very little discipline. We need a lot of patience," he said in the interview late Tuesday in the deserted lobby of a hotel in the Turkish border town of Antakya, on a stopover to meetings with opposition politicians elsewhere in Turkey.
"If we have a battle, some show up without invitation," he said of the fighters' penchant for spontaneous decisions, speaking in fluent German. "They want to take part and shoot."
Idris said he does not have an office in Syria and moves between safe houses because he might be targeted if regime sympathizers might give away his location.
Two hours after he'd settled into a host family's home one recent evening, an aide told him they should go. "He said someone, a stranger, drove by here two or three times with a car," he said of the reason for changing quarters in the middle of the night.
In the Hama region, his laptop battery died and he couldn't Skype with his officers anymore, he said. Elsewhere, there's no cellphone coverage. The officers in the five operations centers are also constantly on the move, Idris said.
"We take the maps with us," he said. "Sometimes we lose something. It's not well organized, but we don't have a choice."
Such travails could boost the new chief's credibility with the fighters.
Abu Moawiya, a former builder who is now a local battalion commander near Maaret Misreen, said he's ready to work with anyone who is based in Syria.
As does Bitar, Abu Moawiya spends much of his time with his men, including on dangerous jobs, such as making homemade bombs by stuffing explosives into metal pipes.
Abu Moawiya insisted that he be identified only by his nom de guerre rather than his full name, fearing retribution against his family by the Assad regime.
Trying to widen support, the new military command will have to finesse its position regarding one of the most effective fighting groups, the al-Qaida-inspired Jabhat al-Nusra, branded a terrorist organization last week by the Obama administration.
The group appears to be popular among rebels, and for fighters like Abu Moawiya, a former al-Nusra member, sidelining it is treason. He said he quit al-Nusra in the summer because it didn't want to accept his friends, but that "our hand is in their hand as we liberate Syria from Bashar."
Idris was trying to walk a middle line, neither embracing nor rejecting al-Nusra. He said the group chose not to be part of the unified rebel command, but that "they are not terrorists."
He estimated that about one-fifth of al-Nusra's fighters are foreigners, but said he believes they will leave Syria once the regime has been toppled. The Syrians in the group, which is believed to number several hundred fighters, could be lured back to mainstream Islam after the war, he said.
The presence of Islamic extremists among the rebels is one of the reasons the West won't equip the Syrian opposition with sophisticated weapons, such as anti-aircraft missiles.
Idris said with such weapons in hand, his fighters could bring down the regime within a month. Without foreign military help, he estimated it could take up to three months. Idris claimed that more than 120,000 armed men are fighting Assad's military, a figure difficult to confirm independently in the chaos of the civil war.
Assad's troops are stretched thin after a 21-month-old conflict. They've also lost ground, particularly in northwestern Syria, but have kept rebels pinned down with air bombardments.
Recent U.S. intelligence reports indicated the regime may be readying chemical weapons and could be desperate enough to use them. Syria is said to have one of the world's largest chemical arsenals, but the regime insists it won't use them.
Idris said Assad "can and will" use chemical weapons unless the international community forces him to leave.
"We know exactly where they are and we are watching everything," Idris said. "But we don't have the capability to put them under our control."