The last secret of Bashar al-Assad’s nuclear program is being packed up and carried out of Syria, under an agreement almost nobody was told about. The news service Axios reported on Monday, on the word of Israeli and American officials, that inspectors from the International Atomic Energy Agency are about to carry nuclear material out of a hidden site in the country, following understandings that the Trump administration negotiated with Damascus and Jerusalem.
The site, referred to in the reporting as Site 99, holds what is left of a program that was supposed to have ended long ago. The material is yellowcake, the milled uranium ore that is the first step toward enriched fuel, useless for a proper bomb on its own but perfectly suited to a dirty one. It is the residue of the Al-Kibar reactor, the plutonium facility built in eastern Syria with North Korean help and destroyed by Israeli aircraft in 2007 in one of the most effective covert strikes of the era. Assad denied the reactor existed until the rubble was on television; the material that survived it stayed where it was, through the civil war and the fall of the regime in late 2024, until Ahmed al-Sharaa’s government took office in Damascus.
The deal, as Axios describes it, took more than a year to assemble and almost came apart several times. After Assad fell, the agency reached a separate access deal with the new government in Damascus, covering the reactor and other nuclear facilities, and it was during that process that Site 99 came into focus. Israel had been watching the site closely and made clear it would not allow the material to remain, warning that it would bomb the site a second time unless the material left the country, or if Damascus showed any sign of reaching for it. Washington and Jerusalem concluded that the least dangerous option was to buy the cooperation of the Syrian government, and the negotiations ran for months, through exchanges of threats and diplomatic letters, before the arrangement was finally sealed a few weeks ago.
The oddest detail, repeated by the officials who spoke to Axios, is that the Syrian government says it did not know the material was there. Officials in Damascus said they knew nothing about any nuclear material being on the site. The people involved in the talks told Axios that the circle of those who knew was extremely small, spread across the three countries, and that the new Syrian government had proved a good partner in the arrangement. Whether Damascus genuinely did not know what the old regime had left in the desert, or found it convenient to say so, the effect is the same: the new Syria has inherited the old one’s secrets, and it is now handing them over.
The deal was also built to contain a third party. Israel, according to the reporting, remained suspicious of Turkey’s position throughout, and the arrangement was meant in part to prevent a confrontation that would have drawn in Ankara, the power that backed the offensive which toppled Assad and the closest patron of the new Damascus government. The removal takes the flashpoint off the table before anyone had to fire a shot over it.
For the Trump administration, the episode is presented as validation of its Syria policy. Axios notes that the deal shows the administration using its close relationship with al-Sharaa, who met Trump in Ankara in July during the NATO leaders’ gathering, to neutralize a crisis quietly. The handshake in Ankara and the handover at Site 99 belong to the same project: a new Syria doing business with Washington.
What almost happened is worth stating plainly. Two decades ago, Israel solved the problem of Al-Kibar with bombs. The material at Site 99 was within reach of the same solution, and Israel said so. Instead, an international inspectorate will walk in, inventory the uranium, and walk out with it, and the world will learn about the whole operation from a news report. Assad’s program, which was meant to end in the same silence it began with, will end with a packing list.
The removal has not been confirmed by the IAEA itself, and the details rest on the word of officials who asked not to be named. But the shape of the story is consistent with everything known about the site’s history. The uranium is leaving Syria quietly. For once in the long story of that program, quiet is the best available outcome.