The Islamic State remains “far from defeated,” one of the nation’s top generals warned Tuesday, seeming to break with President Trump’s assertion that the terrorist group was “99 percent” beaten after four years of U.S.-led military action in Syria and Iraq.

The fear of an Islamic State resurgence — and what analysts say is the near-impossible task of fully eradicating the group — cloud the long-term status of American troops deployed in Syria. It also is the latest sign of the White House and Pentagon’s struggle to stay on the same page in the fight against terror.

Mr. Trump and his top generals also have sent conflicting signals in recent weeks on whether the U.S. believes that countering Iranian proxy groups such as Hezbollah inside Syria is part of the American mission, casting even more uncertainty on the administration’s broader goal and sending mixed messages to allies.

Gen. Joseph F. Dunford, chairman of the Joint Chiefs of Staff, said flatly Tuesday that the Islamic State had lost the vast majority of its physical territory across Syria and Iraq but is evolving into a threat that will be more difficult to stamp out.

“I think we’re all realists in this room, and despite recent successes against ISIS and positive trends, we know there’s actually much work to be done,” he told a gathering of international defense chiefs at Joint Base Andrews in suburban Maryland. “ISIS is far from defeated and has a presence in countries from West Africa to Southeast Asia. Its ideology continues to inspire homegrown violent extremists in many of our countries.

“ISIS is already evolving to implement a more diffuse model, command and control, and operations,” he said. “And they’re looking to maintain relevance by exploiting disenfranchisement and conducting high-profile attacks.”

Hours after his speech, other top military officials downplayed the Islamic State’s strength and stressed that the group as a fighting force capable of capturing and holding territory is all but dead.

“ISIS is territorially defeated,” Army Col. Sean Ryan, spokesman for the American-led coalition against the Islamic State, told reporters at the Pentagon. “We’re degrading them every day. It’s not just killing ISIS fighters. It’s taking away their weapons systems, taking away their logistical support, things of that nature. That’s happening every day.”

Those comments echo Mr. Trump’s declaration earlier this year that the Islamic State was 99 percent eliminated and that final victory was within sight. They also underscore the two different aspects to America’s strategy: Defeating the Islamic State as a physical force, and crushing the ideology that has drawn foreign fighters to the region and inspired terrorist attacks from the United Kingdom to the Philippines.

On the physical front, it’s clear that the group has sustained dramatic losses and is simply no longer able to control the religious caliphate it once ruled from its Syrian stronghold of Raqqa. Officials also say the number of foreign fighters trying to join the group in Iraq and Syria has dropped significantly.

But regional analysts say the notion of entirely eradicating the group — the administration’s stated goal — is virtually impossible.

“Countering and defeating the ideology that inspires this type of violence will be a long-term battle, and the group will probably proliferate and linger outside the Middle East and in other fragile states. … This is not something that can be totally eradicated or defeated,” said Michael Sharnoff, director of Regional Studies at the Daniel Morgan Graduate School of National Security.

“We can deny them the physical real estate … but it’s the ideology that inspires the violence, which many in the West have had a hard time comprehending and identifying,” he said. “There are no easy, quick fixes. This is something leaders all over the world are trying to grapple with.”

The Iran question

Inside Syria and Iraq, the administration also is faced with complex geopolitical questions about the future of Syria and Iran’s influence in the region, even as the Assad government reasserts control over the bulk of the country. Proxy groups working with Tehran, such as Lebanon’s Hezbollah, continue to be a major force in the region and have allied themselves with Syrian President Bashar Assad and his Russian allies. The presence of Hezbollah and Iranian military advisers inside Syria remains a grave concern to Israel, which has looked to Washington and Moscow to guarantee the group and other Iranian-allied forces won’t use Syria as a launch pad for attacks.

But there is little clarity on whether the administration believes part of its overall mission in Syria is to counter Iran. From the military’s point of view, the task is only to defeat the Islamic State.

Col. Ryan told reporters Tuesday that the U.S. would defend itself only if attacked by Iranian-backed groups and said unequivocally that Iran is not the focus of American forces.

“Our fight is with ISIS. … We will defend ourselves if [Iran attacks], but our fight is not with Iran right now. It’s to defeat ISIS,” he said.

Top White House officials have cast the situation differently in recent weeks.

Speaking to the United Nations General Assembly in New York late last month, White House National Security Adviser John R. Bolton said the U.S. will stay in Syria until Iranian troops and proxies are gone — suggesting that the American mission extends beyond simply defeating the Islamic State.

“We’re not going to leave as long as Iranian troops are outside Iranian borders, and that includes Iranian proxies and militias,” he said.

If that indeed is the administration’s long-term plan, then it is likely to cause ripple effects across the region that could bring the U.S. into direct confrontation with Assad and his allies.

Top Syrian officials said this week that after retaking the rebel-held enclave of Idlib in the northwest, they will turn their attention to areas east of the Euphrates River currently held by U.S.-backed Kurdish and Arab militias.

“After Idlib, our target is east of the Euphrates,” Syrian Foreign Minister Walid Muallem said Monday, according to the Iran-based Kayhan news outlet.

Russian Foreign Minister Sergey Lavrov blasted the very idea of a long-term U.S. presence in Syria and said Washington already is attempting to establish a “quasi state.”

“On Syrian territory, there are vast lands east of the Euphrates where absolutely unacceptable things are taking place,” he said. “The U.S. is trying to use these lands through their Syrian allies — above all, through the Kurds — in order to establish a quasi state there.”

Some analysts argue that while a direct military confrontation with the Iranians — and by extension their Russian allies — in Syria is undesirable, the situation has tipped in Tehran’s favor.

“Iran is winning the proxy war. … They’re winning in Syria,” Mr. Sharnoff said.

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