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The final stretch of the IAEA investigation into Iran's past nuclear weaponization work – dubbed the Possible Military Dimensions (PMD) of Iran's nuclear program – came in a two-part development earlier this month. Part I occurred on December 2, 2015: after years of investigating twelve outstanding questions about Iran's past work on military aspects of its nuclear program, with very limited results due to lack of Iranian cooperation, IAEA Director General Yukiya Amano submitted his final report on the PMD. This was in accordance with the timetable set forth by the Joint Comprehensive Plan of Action (JCPOA), concluded between Iran and the P5+1 in mid-July 2015. The JCPOA did not stipulate that the PMD issue had to be resolved to the satisfaction of the IAEA in order to proceed to implementation of the agreement, including the removal of sanctions. It only demanded that a report be submitted.

From late 2011, when the PMD were first included in the IAEA's quarterly report on Iran, Iran stonewalled the IAEA's investigation into this issue. Iran refused to allow entry into suspicious facilities, did not submit full answers to the questions by the IAEA inspectors, and did not allow the IAEA to question key scientists involved in Iran's nuclear program. Still, the IAEA was mandated in July 2015 to submit a final report by December. In his report, Amano concluded, "The Agency’s overall assessment is that a range of activities relevant to the development of a nuclear explosive device were conducted in Iran prior to the end of 2003 as a coordinated effort, and some activities took place after 2003…The Agency has no credible indications of activities in Iran relevant to the development of a nuclear explosive device after 2009." Significantly, at a news conference in Vienna a week before the report was released, Amano said that the report would not be black and white, because while the IAEA had received more information over the past months, gaps remained. According to other diplomats familiar with the investigation, Iran provided little new significant information, and many of the twelve PMD issues were not satisfactorily resolved.

Part II of the PMD closure came on December 15, 2015 when the IAEA Board of Governors (BOG) convened to discuss Amano's report. A week earlier the P5+1 states had submitted a draft resolution to the BOG that stipulated that the IAEA verification activities regarding the PMD issues were completed, basically closing the PMD file. The resolution – which did not mention Amano's conclusions about past weaponization work or Iran's lack of cooperation with the IAEA – was adopted by the BOG by consensus. The resolution was clearly looking toward JCPOA implementation, not back at Iran's NPT violations.

The upshot is that Iran was found guilty of developing a military nuclear capability, with a hint that if Iran had cooperated fully with the investigation, even more incriminating conclusions might have been drawn. Still, Iran was let off the hook, and the PMD file was closed by the BOG. Once the Iran deal is implemented and sanctions are lifted, there will be no leverage to pressure Iran to be any more cooperative with future investigations into possible misdeeds than it has been with the PMD investigation.

What explains this outcome? Because this was an IAEA investigation, it might seem logical to focus on the organization itself when searching for the explanation. Why was the IAEA BOG so willing to close an investigation when the technical secretariat had not received full answers to its questions, and the conclusions they had arrived at were so damning? However, as Amano emphasized, the IAEA is a technical organization with a technical mandate, and it followed this mandate to the best of its abilities, given the constraint posed by the lack of Iranian cooperation, and the limited and evasive answers to the IAEA questions and requests.

The decision in this case was political, not technical, which points in the direction of the P5+1 – the states that negotiated the Iran deal and set the terms for how the IAEA investigation would be framed and integrated into the overall negotiation. Clearly from the outset of the negotiation in early 2014, the P5+1 expected that the investigation into the PMD would be handled by the IAEA and that the P5+1 would not intervene.

While this was a logical decision as far as the technical issues were concerned, less understood at the time was how the information regarding Iran's past deeds would be integrated into any comprehensive and final nuclear deal with Iran. In this sense and despite some official US statements to the contrary, separating the IAEA investigation from the political negotiation seemed to signal willingness on the part of the P5+1 to secure a deal with Iran independently of the PMD investigation. This was especially the case as it became clearer that Iran was adamant about clinging to its narrative of having “done no wrong” in the nuclear realm. When the JCPOA was announced before the PMD issue was finalized, it was clear that the separation meant that the deal was not contingent on getting to the bottom of Iran’s past violations. The P5+1 conceded to Iran's unwillingness to expose its military program, and the IAEA ended up playing a submissive role in the script written and directed by the P5+1.

What will the implications of this decision be down the line?

The IAEA BOG resolution welcomed "Iran's reaffirmation" in the JCPOA "that it will under no circumstances ever seek, develop or acquire nuclear weapons, and Iran's agreement that it will not engage in activities which could contribute to the development of a nuclear explosive device." But how does this square with a result that ignores the conclusion that Iran was a violator of the NPT in the past? Can Iran be trusted to uphold this "reaffirmation" when its own response to the BOG resolution was that the "fabricated" problem of the PMD had finally been swept away? Indeed there does not seem to be any indication in Iran's behavior since the JCPOA was announced in July to support an assessment that Iran is likely to deal any differently with its military ambitions in the future than it has in the past. Iran’s recent tests of ballistic missiles capable of carrying a nuclear payload only increase the sense that there will be no change.

From Israel’s perspective, the result of the PMD investigation is one more indication of the weakness of the JCPOA. While many other states in the Middle East initially welcomed the JCPOA, various signs imply that the Iran deal has brought them little comfort. The effects of whitewashing Iran’s weapons development program will probably only deepen their anxiety. A decade is a very short time in this region's history, and after ten years, with many of the restrictions lifted, Iran could well be on its way to becoming a formidable nuclear foe.