There’s a battle raging inside the Obama administration about whether the United States ought to push away from its goal of toppling Syrian dictator Bashar al-Assad and into a de facto alliance with the Damascus regime to fight ISIS and other Sunni extremists in the region.

As President Obama slowly but surely increases the U.S. military presence on the ground in Iraq, his administration is grappling with the immediate need to stop the ISIS advance and push for a political solution in Baghdad. The 3 1/2-year grinding civil war is Syria has been put on a back burner for now. Some officials inside the administration are proposing that the drive to remove Assad from power, which Obama announced as U.S. policy in 2012, be set aside, too. The focus, these officials argue, should instead be on the region’s security and stability. Governments fighting for survival against extremists should be shored up, not undermined.

“Anyone calling for regime change in Syria is frankly blind to the past decade; and the collapse of eastern Syria, and growth of Jihadistan, leading to 30 to 50 suicide attacks a month in Iraq,” one senior Obama administration official who works on Iraq policy told The Daily Beast.

In effect, the American government has been in a limited partnership with the Assad regime for almost a year. The U.S., Russian, and Syrian governments made a deal last September to destroy Assad’s stockpile of chemical weapons—and relied on Damascus to account for and transport those weapons, in effect legitimizing his claim to continued power.

As far back as last December, top White House officials, including Deputy National Security Advisor Tony Blinken, have suggested that the rising threat of extremism was creating a “convergence of interests” between the U.S., Russia, and its allies in the Iranian and the Syrian governments to come to a political deal before the Islamists became too powerful.

“The Russians have a profound interest in avoiding the emergence of an extremist Syria, a haven for extremist groups,” Blinken said at the time. “Many of Syria’s neighbors have the same incentive, and of course we have a strong reason to want to avoid that future.”

But the view that Assad can somehow be a partner of any kind is vigorously disputed by other senior U.S. officials, especially those who work or have worked on Syria policy. They say the problem of extremism in the region can only be solved by removing Assad from power. Not only is the Assad regime a magnet for terrorism, they argue, but Assad and the extremists inside Syria are working together.

“The people who think Bashar al Assad’s regime is the answer to containing and eventually eliminating the Islamic-based threat do not understand the historic relationship between the regime and ISIS. [They] don’t understand the current relationship between Assad and ISIS and how they are working on the ground together directly and indirectly inside Syria,” Robert Ford, the recently departed U.S. ambassador to Syria, told The Daily Beast. “The people who think Assad’s regime survival is essential have not explained how his survival would solve the problem of extremism in Syria.”

The Syrian Air Force has conducted strikes inside Iraq. But the Syrian Arab Army avoids attacking ISIS held areas in Syria—where the group’s headquarters and larger bases are—and rarely fights ISIS at all inside its own country. ISIS sells the regime oil directly from fields it controls in northern Syria. ISIS and the regime reportedly coordinate their attacks on the Free Syrian Army.

Some administration officials are also suggesting that Iran could be a partner in a post-war Syria, helping to ensure security there during a transition period, after which Assad would negotiate his own departure.

Sen. John McCain, who is traveling in the region this week, called that idea ridiculous.

“There is no negotiated settlement that is going to lead to the departure of Bashar Assad,” unless the balance of power on the ground is shiifted towrad the rebels, Sen. John McCain told The Daily Beast. “That hope ended a long time ago.”

McCain met Tuesday in Turkey with top leaders of the Syrian Opposition Coalition and the leaders of the FSA’s Supreme Military Command, who have been begging the Obama administration for more and better weapons, including anti-aircraft weapons to protect civilians from the regime’s ongoing barrel bomb campaign.

The crisis in Iraq is a disaster for the moderate rebels, including the undermanned and under-resourced FSA. Their enemies in ISIS are growing stronger. And Assad has been drawn closer together to the Iraqi government, adding to his alliances with Russia, Iran, and Hezbollah.

“The events in Iraq have had serious consequences for Syria and the Free Syrian Army,” McCain said. “What ISIS is picking up in Iraq they are bringing back into Syria and using directly against the FSA. The FSA was losing some people because of their failure to get the kind of assistance they need. Some of their fighters are moving over to ISIS because ISIS is winning.”

If those inside the Obama administration arguing for regime preservation in Syria win the day, he argued, the U.S. will be playing right into Assad’s hands.

“It’s obvious that Bashar al Assad’s strategy is to present us with a choice of ISIS or him so that eventually we will choose him,” said McCain.

In Iraq, the United States has begun to deliver troops and aircraft to help the embattled government in Baghdad. Iran and Russia are supplying planes and forces of their own. And in the meantime, Assad’s planes are delivering air strikes on Iraq. To McCain, that amounts to an American alliance with those countries, whether that was intentional or not. (To be clear: McCain is also for providing military assistance to Baghdad; he’s just for hitting ISIS in Syria at the same time.)

“I don’t think the administration believes that they are [on the same side as Iran, Russia, and Syria in Iraq], but their actions indicate that by cooperating with them, you would have to assume that de facto they are on the same side,” he said.

The Sunni-Shi’ite split in the Islamic world adds to this sense. Iraqi Prime Minister Nouri al-Maliki and Assad are both Shi’ites; ISIS is Sunni. So the Sunni populations both in Iraq and Syria view the U.S. military assistance to the Iraqi government as America taking sides against them in the greater Sunni-Shia regional conflict, according to Tareq al-Hashimi, the Sunni vice president of Iraq, who is in exile in Turkey.

“It’s a really annoying development. The U.S. is in the process of committing itself to another set of grave mistakes. Definitely we consider all this military support to Nouri al-Maliki as an alliance with Iran against the Arab Sunnis,” he told The Daily Beast in an interview Wednesday. “And all of the Sunni Muslims around the globe are going to be angry and they are going to see all this interference in our internal issues, we will criticize and condemn this intervention from the U.S. At least they should be neutral.”

Oubai Shahbandar, spokesman for the Syrian Opposition Coalition’s Washington, D.C., office, told The Daily Beast that for the moderate opposition, any cooperation with Iran, Russia, and the Syrian regime is taking U.S. policy in the wrong direction.

“The U.S. has natural allies with the Syrian revolutionary forces, while Iran has contributed to the deaths of as many Americans as al Qaeda,” he said. “Stability in Syria means a strategic partnership between the U.S. and Syrian freedom fighters, not with an Iranian regime that continues to sponsor international terrorism.”

Ford said that the war on ISIS in Iraq, no matter who is fighting it, might not be all bad for the Syrian rebels because it could result in damaging ISIS over time.

“If ISIS takes hits in Iraq, that’s not bad for the FSA because that could force ISIS to shift resources back from Syria into Iraq at some point,” he said. “It’s only a problem if the administration decides Assad is part of the solution to solving ISIS, but I don’t think they have come to that conclusion, yet.”

The Obama administration last month announced a request for $500 million to drastically increase the training and equipping of selected brigades inside the Free Syrian Army. It was hailed by Secretary of State John Kerry as a major step toward bolstering the moderate rebels, now losing the war on two different fronts.

Standing next to SOC President Ahmed Jarba in Saudi Arabia last week, Kerry presented the new aid as a good way to solve the ISIS Iraq crisis, not as a way to solve the Syrian civil war.

“The moderate opposition in Syria… has the ability to be a very important player in pushing back against [ISIS’s] presence,” Kerry said.

But that the $500 million in assistance, if approved by Congress, won’t even be appropriated until at least January because no spending bills are likely to pass Congress until after the U.S. midterm elections. The money was requested as part of the fiscal 2015 Overseas Contingency Operations account, a tenth of the $5 billion counterterrorism fund President Obama announced in his West Point speech in May.

Lawmakers in both parties are skeptical about Obama’s commitment to the program because the fund was announced with no congressional consultation at all. The long process of programming of the money would mean its effect would not take hold until well into next year.

In the meantime, the FSA and moderate rebel groups are likely to be increasingly outgunned and outmanned by ISIS over the next months. So far, the Obama administration has ruled out striking ISIS in Syria, where the terror group is the strongest, said Andrew Tabler, senior fellow at the Washington Institute for Near East Policy.

“Our inability to deal with ISIS even in Iraq, combined with a lack of working with moderates in Syria, allowed ISIS to fester,” he said. “Now that has led to not only a full-blown crisis but has greatly harmed our ability to get a solution to the Syrian civil war in general.”

Eli Lake contributed reporting to this article