In a classified report, mandated by the fiscal 2019 defense authorization and sent to Congress just before Thanksgiving, Defense Secretary Jim Mattis repeated his objection to the threat. Cutting off Turkey, whose defense industry produces significant F-35 components, Mattis said, would cause major delays in overall production of the new generation combat plane, according to congressional officials who spoke on the condition of anonymity about the sensitive issue.

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The State Department, in charge of foreign military sales, says it is continuing to try to persuade Turkey to buy an alternative missile defense system, the Patriot. Turkey says its needs are urgent and the United States has dithered for years and never made a serious Patriot offer.

“It’s a done deal,” Turkish Foreign Minister Mevlut Cavusoglu said of the S-400 purchase during a visit here last week.

Separately, Turkey and the United States continue to dispute the U.S. military alliance with Kurdish fighters waging the ground war against the Islamic State in Syria. Turkey considers the Kurdish forces to be terrorists and has shelled Kurdish positions in U.S.-controlled eastern Syria at least twice in the past month, in response to what it said were cross-border Kurdish attacks on its troops.

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Last week, Mattis told reporters U.S. forces were setting up observation posts along the border “to call the Turks and warn them” if they see any threat coming from within Syria.

But on Saturday, Turkish Defense Minister Hulusi Akar said he has repeatedly told the Pentagon the observation posts are a bad idea. “It could lead to the perception that U.S. soldiers are somehow protecting terrorist YPG members” from a Turkish counterattack, he told Anadolu, the Turkish news agency.

YPG are the Turkish initials for the People’s Protection Units, the armed wing of the Syrian Kurdish political movement. Turkey says they are part of the militant Kurdistan Workers’ Party, or PKK, the Turkey-based political organization fighting for autonomy within the Turkish state. The United States considers the PKK terrorists, but disagrees that the two groups are one and the same.

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“We expect that our U.S. allies cut their relations with the terrorist YPG,” Akar said.

During his meeting here with Secretary of State Mike Pompeo and White House national security adviser John Bolton, Cavusoglu said he also repeated Turkey’s call for the extradition of Muslim cleric Fetullah Gulen, the Turkish citizen who lives in Pennsylvania as a permanent U.S. resident.

Turkey has charged Gulen with responsibility for a failed 2016 coup attempt. Since then, it has arrested or fired from government employment tens of thousands of Turks charged with belonging to what it calls Gulen’s “terrorist organization.” Cavusoglu said he presented Bolton with a list of 83 other Turkish nationals in this country that it wants extradited. The list, he said, was requested by President Trump during a recent telephone conversation with Turkish President Recep Tayyip Erdogan.

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The list has long been in possession of the Justice Department, which has repeatedly said the Turks have presented insufficient evidence to justify the extraditions.

Brunson’s release, after more than two years of detention on charges of terrorism related to both Gulen and the PKK, at least temporarily released some of the built-up pressure in the relationship. U.S. appreciation, Trump tweeted at the time, “will lead to good, perhaps great, relations between the United States & Turkey!”

Washington and Ankara have also found themselves more or less on the same side of the international controversy over the killing of Saudi Arabian journalist and Washington Post contributing columnist Jamal Khashoggi in Istanbul last month, although Trump has declined to blame Saudi Crown Prince Mohammed bin Salman while both the CIA and Erdogan have indicated he was responsible.

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Turkish officials have said the Khashoggi case should not affect Turkey’s bilateral relationship with the United States, even if Trump prevails, over strong sentiment in Congress, in his reluctance to punish the Saudis. Trump and Erdogan will both attend the G-20 summit later this week in Argentina, along with the crown prince and Russian President Vladi­mir Putin.

The situation on the Turkey-Syria border poses the most immediate threat of a serious breach in relations, as Turkish troops are poised inside Syria west of the Euphrates River, and just across the border on the U.S.-held eastern side, where much of the territory seized from the Islamic State is controlled by the YPG.

The F-35 problem is unlikely to provoke a shooting war, but poses a far greater risk over the medium and long term.

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Turkey believes, and the United States agrees, it lives in a dangerous neighborhood and needs a reliable missile defense system. When the Syrian war next door was particularly hot in 2015, Turkey turned to NATO for defense. Syrian missiles had struck Turkish territory, and Turkey shot down a Russian plane that strayed across its border while aiding the forces of Syrian President Bashar al-Assad.

Turkey asked to buy Patriots from the United States, but the request has languished amid Turkish demands for the inclusion of technology transfers neither the U.S. manufacturers nor the U.S. government want to provide. Ankara began negotiating with a Russian defense industry eager to expand its own sales, particularly to a NATO country.

As soon as it was clear that a Russian sale of the S-400, its most advanced system, was in the offing, red lights began flashing at NATO and in Washington.

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Turkey, one of the original members of the consortium of eight alliance countries that signed up to produce component parts of the F-35, including elements of the fuselage, landing gear and cockpit, also signed up to buy 100 of the aircraft. The plane is designed to avoid systems like the S-400. Putting them side by side in Turkey is seen as a technological gift to the Russians.

Congress has already passed legislation to impose sanctions on any country that buys sophisticated Russian weaponry. Passage of new legislation to prevent F-35 deliveries already in motion would presumably end Turkey’s co-production and at least temporarily shut down assembly lines for the thousands of planes ordered by the United States itself and by other countries.

Turkey’s first two F-35s, with ownership already transferred and pilots in training, are scheduled for delivery next year, just a few months before S-400 installation is due to begin.