As regime planes and helicopters ratchet up a massive offensive now in its second week, alliances in southern Syria’s rebel-held ground are beginning to shift under the weight of increasing foreign support and long-simmering ideological differences.

The relationship between al Qaeda franchise al Nusra Front and the moderate, secular Free Syrian Army (FSA) has, at least in the southwestern city of Daraa, been fairly high functioning. The two groups have long fought alongside one another against the Syrian regime. They also have close family ties: in Daraa, many of the men who fight with the FSA have friends and kin who fight with Nusra.

But over the past weeks a combination of internal and external factors have dialled up the tension on a relationship that was complicated to begin with.

“It’s as close as possible to the Cold War right now,” Chief of Operations for the al-Omari Brigade Malouh al-A'esh told VICE News.

Malouh al-A'esh, Chief of Operations for the al-Omari Brigade, part of the FSA's Syria Rebels Front

His brigade, part of the Syria Rebels Front, is one of several moderate FSA factions in Daraa to have recently been gifted with American-made TOW — tube-launched, optically-tracked, wire-guide — missiles.

These wire-guided anti-tank missiles, capable of piercing the armor of any vehicle used by the Syrian army, aren’t game-changers in the usual sense: the regime still owns the air. But they have unsettled the checks and balances that enabled the secular FSA and jihadist Nusra to coexist so easily for so long.

Nusra's identity is in flux. While for much of the war it has been the better-armed and better-funded fighting group — something that helped it attract fighters — that is no longer necessarily the case. Some parts of the FSA are now much more heavily armed, and the American weapons they’re fighting with are a stark reminder of America’s interests in this war.

“For US intelligence, the primary concern is jihadism — that al Qaeda could get a permanent place in Syria,” Josh Landis, director of the Center of Middle East Studies at the University of Oklahoma told VICE News. “But al Qaeda is doing this, and America is worried.”

So far, despite the fact that the FSA’s biggest backer wants to take down its erstwhile ally, those factions that have received US support have kept their eyes on the prize — eliminating the Assad regime.

“The primary objective is the fight against the regime, until we achieve the liberation of Syria. Any problems or obstacles that take us away from this goal will be treated with firmness,” said al-A'esh.

One of those problems is rapidly becoming the elephant in the room: the ongoing detention of a high-ranking FSA commander, Colonel Ahmed al-Ni’ma.

Members of Nusra had arrested al-Ni’ma and several others in early May, accusing the colonel of throwing the strategically vital May 2013 Battle of Khirbet Ghazaleh to the regime at the request of foreign backers.

Several of the FSA’s more moderate factions — including the Yarmouk Division, another group to have received American TOWs — quickly posted a statement online, calling off collaboration between the FSA and Nusra. Signatories included 59 separate factions and the catch all “all factions operating in the southern front.”

But as quickly as the statement was posted, it was removed — some factions did not stand behind it. Rather than driving a wedge between the FSA and Nusra, the incident exposed some of the differences bubbling just below the surface in the collection of groups that fight under the banner of the FSA.

Jabhat al-Nusra fighters near one of their headquarters in the eastern countryside of Dera'a

After nearly two weeks of heavy fire from their shared enemy, the relationship between the two rebel groups seems to be holding — but its strength depends on who you ask.

“Fighters from the FSA and Nusra work together in the free areas and relations between them are very natural,” Mohammed Ktefan, a Nusra fighter from Daraa, told VICE News.

Ktefan described the ongoing battle in Nawa and the recent battle in Manshia, in the countryside around Daraa, as examples of the FSA and Nusra fighting together.

“This talk about controversies and clashes is just propaganda. It doesn’t exist on the ground,” he said.

But on the ground in Lajat, in the northeast of Daraa province, al-A’esh had a very different take on things.

“Currently there is cooperation between Nusra and some factions of the FSA, where these factions lack ammunition and heavy weapons,” he said. “This is happening now in Nawa and it happened previously in the battle of Manshia.”

Fighters fight where the heavy weapons are, agreed an activist from the Tahrir Souri media network, who operates anonymously for his own and his family’s protection. Any FSA-Nusra collaboration that’s happening now isn’t about ideological tolerance, he said, but about a means to an end­ — specifically to the Assad regime.

“At the beginning, all the FSA fighters who joined Nusra did so because it was better-funded, had better weapons, and was more organised. It offered a better chance to defend your country. But once another alternative presents itself, the more moderate Syrian members of al-Nusra will come back.”

When and how they do seems to depend on the flow of Western weapons into the country — something this activist believes has the potential to turn the war around.

“Maybe it’s not too late to fix the problems caused by the delay in helping the rebels,” he said. “Once the right people are armed, the moderates will go back to the FSA and a stronger FSA will fight the regime and al Qaeda.”

For now, commanders like al-A’esh are most concerned with keeping the “Cold War” between the FSA and Nusra from getting hot.

“Right now the most tense areas are East Ghariyah and al-Karak, where there have been demonstrations against the arrests,” he said. “There are efforts by some dignitaries to mediate with Nusra and resolve this problem.

“God forbid there would be a war between the FSA and Nusra. It would be a disaster for everyone, and a victory for the regime.”

Follow Sara Williams on Twitter: @saraewilliams