There is nothing conclusive on an Iranian nuclear weapons program, but the circumstantial evidence is compelling. A quick rundown:
1. Their enrichment program was completely clandestine until it was exposed by Libya’s revelations about the AQ Khan network. Why is it necessary for a civilian program to be clandestine - especially to the point of burying and hiding facilities (Natanz) at great expense?
2. The IAEA discovered a report on the shaping of uranium metal hemispheres and the Iranians have not explained how they got the paper or why they have it and have yet to provide a copy to the IAEA. The only purpose for such information is a uranium implosion device. This is one of the outstanding issues that’s been in every IAEA report for several years now: http://www.isis-online.org/publications/iran/IAEAreport22Feb07.pdf (That’s the english version of the report Amir). Read the other outstanding issues Iran hasn’t answered, such as plutonium separation experiments - another weapons-related technology.
3. Iran is building the IR-40 “research” reactor at Arak. The Iranian’s claim its for research and isotope production, but virtually every reactor in the world of similar design has been used for plutonium production. It is, in fact, tailor made for that purpose. Iran could produce the isotopes it needs with smaller reactors could not easily product plutonium. See more here: http://www.armscontrolwonk.com/1300/technical-cooperation-for-arak
4. The Iranian nuclear program does not make economic sense even though economics and energy independence are primary reasons Iran says it needs nuclear power. For more see this summary of a doe report (the full report is not yet available because the authors are trying to publish it): http://www.globalsecurity.org/wmd/library/news/iran/2006/iran-060421-usia02.htm
5. The link above also discusses Iranian uranium reserves, which are quite limited. The Iranians are spending billions on enrichment when it will run out of reserves in a decade or two and be force to import ore anyway. Why not just import fuel - it’s cheaper and easier and Iran would not have to deal with long-term waste storage.
6. Iran did not declare a research center at Lavizan was nuclear-related under its safeguards agreement. When it was revealed that nuclear-related material was shipped to the site and the IAEA asked to inspect it, all the buildings were razed and the ground was scrapped clean. The Iranian explanation for this was that the site was bought by the city to turn into a park. See more here including satellite images: http://www.isis-online.org/publications/iran/lavizanshian.html
7. The IAEA, under the safeguards agreement with Iran, is only allowed to inspect “declared” sites. A declared site is one that Iran declares is part of its nuclear program. The problem with this kind of arrangement is obvious. Obviously, Iran only declared sites it couldn’t reasonable argue were not nuclear-related, and sites that appeared obviously civilian in nature. This is a major of weakness of the NPT - it relies on nations honestly declaring all their nuclear facilities. For example, there is another undeclared site at Parchin (in addition to Lavizan) the IAEA suspects is nuclear related, but the Iranians have refused to grant access: http://www.isis-online.org/publications/iran/parchin.html
8. Iran is building an extensive enrichment infrastructure, but so far only one reactor is being built to service that infrastructure. Iran has claimed they plan to build 20 or more reactors, but have not yet contracted for them much less broken ground. A typical nuclear reactor takes a decade or more to build. So Iran will have all this enrichment capability and only one reactor for it for at least the next 10-20 years. Considering how dire the Iranians claim their energy needs are, why aren’t they building the reactors first, fueling them with cheap uranium purchased on the open market, and then developing an enrichment infrastructure to support them? Putting the cart before the horse in my view. Meanwhile, Iran’s petroleum sector infrastructure continues to deteriorate. It’s ironic that Iran uses this deterioration and the effects its having on domestic energy supply as proof that it needs nuclear energy.
There are other issues as well, but I think those listed above are most of the major ones. Does it add up to conclusive evidence? No. Every point listed above could have an innocuous explanation, or be countered with appropriate evidence, but the Iranians have consistently been deceptive about both their intent and their actual programs. Iran could dispel much of the evidence above if it were false, yet it either chooses not to or cannot. Considering all the talk of attack by the US or Israel (talk that I think is overblown), one would think Iran would want to increase transparency to erase any doubts, and therefore any justification for an attack.
Now, one thing I’ve said repeatedly is that the evidence fits another possibility - in my view better than an actual Iranian weapons program. It’s my belief that Iran intends to develop the technology and capability to make a nuclear device without actually doing so. Although a parallel clandestine bomb-making program is a possibility (and Amir, the IAEA will never find it because it is not allowed to conduct snap inspections on any suspect site that is not declared), I think it’s more likely Iran has a small R&D program on weapon design (and therefore easily hidden) and will only weaponize if it feels it is necessary. Basically, I think they want to be where Japan and Brasil are - have an advanced civilian program that will allow them to build a bomb in less than a year.
And we can make comparisons to Iraq here as well. We now know that Iraq, or rather, Saddam, wanted his neighbors, primarily the Iranians and Israelis, to believe he still had WMD as a deterrent. So he was at the same time trying to convince one audience he had WMD while at the same time trying to convince another he did not. His calculus was that since he destroyed all his weapons, the UN would not find enough evidence to justify an attack. Of course, he miscalculated. We must be cautious that Iran is not similarly miscalculating. Saddam never really believed the US would invade until literally the eve of the war - he expected France and Russia, whom he had bribed handsomely, to prevent a war. Similarly, Iran believes the US will not and cannot effectively attack it.
Things to ponder.
For those who haven’t yet, please read the Iraqi Perspectives Project on the Iraq war. ( http://www.jfcom.mil/newslink/storyarchive/2006/ipp.pdf ). It’s an excellent analysis of the regime’s decision-making process based on interviews and captured documents. Much of it relates to the military portion of the campaign, but there are important WMD bits in there (Chemical Ali was interviewed, for example) and along with the Duefler report provides a convincing explanation of why and how both the US and Iraq miscalculated. The lessons are very important considering the current crisis with Iran, where misunderstandings and miscalculations also abound.
1. You should observe the US government's attitude towards any Iranian project from an Iranian perspective and you would easily find out why the Iranian government decided to go clandestine. The most relevant example is the Bushehr Nuclear Power Plant. Its construction started before Iran's revolution and it is not yet complete, because different companies decided not to complete the project under US pressure. Nuclear power is not the only example; most other strategic projects follow the same trend. More examples: steel-production and vaccine-related projects. (Javad Zarif's talk in Princeton University provides more detail, minute 39:00)
Now, if you were an Iranian government official, and wanted to produce nuclear fuel, and were sure that it'd be opposed by US, would you buy the equipment from Britain or black-market? Apparently, you wont ink an agreement that will be unilaterally terminated under US pressure. Right?
This is why a covert program is not necessarily an illicit one.
In fact, I can draw an exactly opposite conclusion:
Since Iran's covert program was never diverted towards weapons program during the so-called 18 years of concealment, while it easily could, others can be more easily assured that it'll not be diverted in the future: If it was a weapons program, they should have at least taken few steps towards that path, right? IAEA says that they haven't.