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A clash between Iranian-backed Houthi fighters who were attacking a commercial freighter and U.S. Navy helicopters responding to the ship’s distress call ended on Sunday morning with the killing of all the crew members on three Houthi boats, the Pentagon said, a sharp escalation of violence at a moment when the White House is considering direct strikes on Iran’s proxies in the Middle East.

It appeared to be the first time that American and allied forces patrolling the Red Sea, a critical waterway for oil and other shipments, have engaged in a deadly firefight with the Houthis since their attacks on ships began in October, following the outbreak of the war between Israel and Hamas. President Biden has said he wants to avoid direct military attacks on the Houthis in Yemen, to avoid escalating a Middle East conflict that is already threatening to spread throughout the region.

But in the fight that broke out on Sunday morning, the Navy forces had little choice, at least according to the account given by United States Central Command.

The Houthis had launched an attack on the freighter, the Maersk Hangzhou, a Singapore-flagged container ship, and were attempting to board it. As the ship’s security forces tried to hold the attackers at bay, helicopters from the U.S.S. Eisenhower carrier group arrived to chase them away and the Houthis opened fire on them.

“The small boats fired upon the U.S. helicopters with crew-served weapons and small arms,” Central Command said in a statement. “The U.S. Navy helicopters returned fire in self-defense, sinking three of the four small boats, and killing the crews.” Central Command did not say how many had been killed, but in a statement later on Sunday the Houthis said that 10 of their fighters were dead.

“The American enemy bears the consequences of this crime,’’ they said in a statement, and “its military movements in the Red Sea to protect Israeli ships won’t prevent” the Houthis from “performing their religious, moral and humanitarian duty in support and aid of those who have been wronged in Palestine and Gaza.”

The Houthis say they are disrupting shipping to support victims of Israel’s war in Gaza. Displaced Palestinians living in a tent outside the European Hospital in Khan Younis, southern Gaza, on Sunday.Credit…Agence France-Presse — Getty Images

The incident now presents a difficult choice for Mr. Biden and his administration. Senior officials said they must decide whether to strike Houthi missile and drone sites in Yemen, or wait to see whether the Houthis back off after the sinking of three of their fast boats and the deaths of their fighters.

Ten days ago, the administration declassified intelligence indicating that Iranian paramilitary groups were coordinating the Houthi attacks, providing targeting information about commercial shipping passing through the waterway and the Suez Canal. Israel is heavily dependent on Red Sea shipping traffic.

In response to the attacks, the United States has created a multinational naval task force to protect commercial ships in both the Red Sea and the Gulf of Aden.

The effort, known as Operation Prosperity Guardian, so far includes about 20 countries, among them Britain, Canada, France, Italy, the Netherlands, Norway, the Seychelles and Spain. Most Arab states have declined to join, with the exception of the tiny Gulf state of Bahrain, which hosts a major American naval base, home to the Fifth Fleet, and recently concluded a security agreement with the United States.

Senior Pentagon commanders have been pressing for more aggressive action against the range of Iranian proxies that are attacking American forces, including in Syria and Iraq. Last week, the United States struck a base in Iraq used by Kataib Hezbollah after an attack that injured three U.S. troops, leaving one in critical condition.

But the most urgent problem appears to be in the Red Sea, where the Houthis have launched dozens of missile and drone attacks against commercial ships in response to Israel’s war against another Iranian-backed group, Hamas.

While U.S. forces have struck missile and drone launching sites in Syria and Iraq, Mr. Biden has been reluctant to order the same against Houthi bases in Yemen. The caution is driven by many considerations, but chief among them is that Saudi Arabia wants to move beyond its costly war in Yemen. Escalating the conflict with the Houthis, who control the capital, Sana, and much of the country’s north, could sink a painstakingly negotiated truce.

Houthi troopers in Sana, Yemen, on Saturday.Credit…Yahya Arhab/EPA, via Shutterstock

“Everybody is looking for a way to de-escalate tensions,” Tim Lenderking, the U.S. special envoy for Yemen, said in an interview earlier this month. “The idea is not to engulf the region in a wider war, but rather to use the tools available to us to encourage the Houthis to dial back their reckless behavior.”

At least, that was the strategy until Sunday.

While the United States had shot down Houthi missiles and drones, deployed warships and created the task force to protect shipping, the one thing it had not appeared to do was engage directly with the Iranian-backed militia. That self-imposed moratorium ended with the clash to protect the Maersk ship.

Pentagon officials have worked up detailed plans for striking missile and drone bases in Yemen, and some of the facilities where fast boats of the kind used to attack the Maersk container ship appear to be tied up. But there is some concern that such strikes would play into Iran’s game plan.

“I have doubts on what strikes would do,” said Adam Clements, a former U.S. Army attaché for Yemen. “The Iran-Houthi relationship greatly benefits from conflict, so why create more?”

But several senior retired U.S. officers with experience in the Gulf region say it is essential to re-establish American deterrence, a view echoed by many in the Pentagon. In 2016, the U.S. struck three Houthi missile sites with Tomahawk cruise missiles after the Houthis fired on Navy and commercial vessels. The Houthis’ attacks stopped.

The situation today is different. The Houthis have vowed to continue attacking until adequate supplies of food and medicine are allowed into Gaza, where a humanitarian disaster has been unfolding since the Israeli assault began. The assault followed the Hamas-led Oct. 7 attack on Israel that, Israeli officials say, killed 1,200.

In Israel shortly after midnight on Monday, sirens sounded across the central part of the country warning of incoming rocket fire from Gaza.

So far the administration has bet that assembling the international naval task force in the Red Sea is the best way to isolate the Houthis, and reduces the group’s ability to cast itself as fighting the United States or Israel.

An Israeli missile boat in the Red Sea, off the coast of the Israeli port city of Eilat, on Tuesday.Credit…Alberto Pizzoli/Agence France-Presse — Getty Images

The countries that are participating — and many that are sitting on the sidelines — have both a commercial and a security stake in the initiative. Maersk had just resumed shipping before the attack on the Hangzhou; it has now suspended shipments again.

Yemeni political analysts, and the Houthis themselves, have dismissed the task force as an ineffective exercise that will do little to deter the Houthis, who say that they crave a direct confrontation with the United States.

The Pentagon has a separate concern: deterring attacks on U.S. forces.

“The bigger issue is that the U.S. since early October has also been accepting as normal persistent Houthi missile and drone attacks” on the Red Sea, said Vice Adm. Kevin Donegan, a retired Fifth Fleet commander.

“Not responding when U.S. forces are attacked in any fashion risks the lives of U.S. sailors and marines if a missile were to make it past U.S. defenses,’’ he said. “It also sets a new precedent that attacking a U.S. ship carries low risk of retaliation and as we have seen invites more attacks from the Houthis.”