Just put yourself in Iran’s shoes:I don't have answers to much of this. My general inclination is that Iran will be less likely to negotiate and generally uncooperative, but that depends on internal Iranian politics and the perception of the players of losing face and many other variables.
You have just been notified unequivocally that the United States and Israel have declared war on you and have successfully carried out a first strike. The debate about whether or not to launch a strike against Iran has been answered — just not in the way most people expected, with bombs.
This comes just a few days before you sit down to negotiate with Americans and others over your nuclear program. Will you be intimidated and therefore demonstrate more willingness to compromise? Or will you play either a stalling game or perhaps a more belligerent game until you can improve your negotiating position?
From this point on, will you be more or less likely to cooperate with the IAEA? Will the Non-proliferation Treaty (in which Iran agreed not to build a nuclear weapon in return for international protection against any nuclear powers) seem like a reassurance or a threat?
Will you retaliate by launching a cyber counter-attack against one or more large U.S. facilities (dams, power plants, refineries, public utilities, nuclear facilities, etc.) which, as the NYT story acknowledges, are known to be vulnerable to cyber attack. Although Iran’s capabilities are hugely overshadowed by those of the United States and Israel, cyber warfare may be an attractive way to level the playing field — the ultimate in asymmetric warfare. U.S. interests, of course, are not all located in the continental United States.
Will you (Iran) cut back your nuclear development or double down on your efforts? (Part of the answer to that question depends on resources. If Iran has been holding back, which is not impossible, then it has some capacity to actually speed up its efforts; if Iran has few or no intellectual, material and scientific reserves, its choices may be quite limited; that seems to be the working assumption of the authors of the worm.)
How does the Iranian leadership now deal with the faction that has been arguing in favor of going for a bomb (rather than just building a break out capacity)? Are the hardliners weakened by this or strengthened? Has the Green Movement and the reformist opposition been strengthened or weakened by this?
I'm wondering about motivations in the US, particularly for those who cooperated with the Times reporters. Some of the material in the article must be classified. So either someone talked inappropriately or the administration was happy to have the information leaked. We're not hearing anything that would indicate either of these alternatives is the case, like a great uproar about unauthorized release of classified information. But there could be quiet or an uproar whether the administration leaked the information or not. That would depend on the message they wanted to send, both to unauthorized leakers and to the Iranians.
If the administration was okay with the leak, they are sending a message of strength with an indication that they don't want war. It leaves open the possibility that other worms have been developed. And in that case, they are calculating that Iran will become more, not less, cooperative in view of the US and Israeli capabilities. It leaves open the question of attack, although the public discussion would lead Iran (and the rest of us) to believe that attack is less imminent than it might have been a year ago, although the Israeli talk then could have been posturing. Complicating things is whatever might be going on between the US and Israel relative to a settlement with the Palestinians, which could include statements by the US of unacceptable Israeli actions.
If they're not okay with the leak, there would be no reason to make that public. Iran now knows of US and Israeli involvement, although they must have suspected that. If an investigation is necessary, it will be conducted quietly. We might not even hear when the leaker is fired.
Another thing I've wondered about is whether clandestine nuclear commerce connections can be traced by the spread of Stuxnet. India, Indonesia, and other countries have reported Stuxnet. It is reported to be spread by thumb drives. We don't know how it got into Iran, whether the infection spread from those other countries or the other way around. But those who spread it do know the route of infection and therefore may be able to get additional information about the underground nuclear network.