“There were a lot of mistakes made the first time,” said an American official, avoiding any acknowledgment that the United States played a role in the cyber attack on Iran. “This was a first-generation product. Think of Edison’s initial light bulbs, or the Apple II.”

Not surprisingly, the Iranians are refusing to sit back and take it — which is one reason many believe the long shadow war with Iran is about to ramp up dramatically…

The big hitch in these containment strategies is that they are completely useless if Iran ever slips a bomb, or even some of its newly minted uranium fuel, to a proxy — Hezbollah, Hamas or some other terrorist group — raising the problem of ascertaining a bomb’s return address. When the Obama administration ran some tabletop exercises soon after coming to office, it was shocked to discover that the science of nuclear forensics was nowhere near as good in practice as it was on television dramas. So if a bomb went off in some American city, or in Riyadh or Tel Aviv, it could be weeks or months before it was ever identified as Iranian. Even then, confidence in the conclusion, officials say, might be too low for the president to order retaliation.

The wisdom of a containment strategy has also taken a hit since the revelation of the plot to kill the Saudi ambassador. Emerging from a classified briefing on the plot, a member of Congress said what struck him was that “this thing could have gotten Iran into a war, and yet we don’t know who ordered it.” There is increasing talk that it could have been a rogue element within the Quds Force. If so, what does that say about whether the Iranian leadership has as good a hand on the throttle of Iran’s nuclear research program as Washington has long assumed?…

But now the element of surprise is gone. The Iranians are digging their plants deeper underground, and enriching uranium at purities that will make it easier to race for a bomb. When Barack Obama was sworn into office, they had enough fuel on hand to produce a single weapon; today, by the I.A.E.A.’s own inventory, they have enough for at least four. And as the Quds Force has shown, sabotage and assassination is a two-way game, which may ratchet up one confrontation just as Americans have been exhausted by two others.