We could call this A Tale of Two Facilities. Iran launched an unprecedented direct attack on Israel in retaliation for the targeted strike on IRGC and Hamas commanders. That attack did little damage despite a volley of well over 300 missiles and drones, thanks to the regional defenses and the several hours of lead time necessitated by Iran's launch from its own territory.

That demonstrated the facility Iran has for offensive operations in the region. Israel responded by demonstrating its facility, and as the New York Times hears from officials in Iran and the West, the result shocked the Iranians:

An Israeli weapon deployed in a retaliatory strike against Iran on Friday damaged a defense system responsible for detecting and destroying aerial threats near Natanz, a central Iranian city critical to the country’s secret nuclear weapons program, according to two Western officials and two Iranian officials.

The strike, the Western officials said, was calculated to deliver a message to Iran that Israel could bypass Iran’s defense systems undetected and paralyze them, using a fraction of the fire power Iran deployed last week when it launched hundreds of drones and missiles at Israel. That attack, intercepted by Israel and its allies, caused minimal damage.

Their shock didn't just come from the fact that Israel had denuded their critical Natanz site of effective air defense. It didn't come from realizing just how far Israel could strike without entering its airspace, either. What truly shocked the Iranians is that they had no warning at all before their expensive S-300 system got destroyed from a single strike:

A missile, two Western officials said, was fired from a warplane far from Israeli or Iranian airspace and included technology that enabled it to evade Iran’s radar defenses. Neither the missile nor the aircraft that fired it entered Jordanian airspace, the Western officials said, a gesture meant to keep the kingdom out of the conflict after it helped shoot down Iranian weapons last week.

The two Iranian officials said that Iran’s military had not detected anything entering Iran’s airspace on Friday, including drones, missiles and aircraft. Iran’s state news agency, IRNA, reported that no missile attacks had occurred and that Iran’s air defense system had not been activated.

How precise was the attack? The NYT got a look at satellite imagery of the Natanz S-300 system, both before and after the attack.  The missile strike destroyed the S-300 radar system while leaving other related equipment undamaged:

Images showed that the precision attack at the Eighth Shekari Air Base damaged or destroyed the “flap-lid” radar, which is used in S-300 air defense systems to track incoming targets. ...

Other areas of the air base and adjacent airport also appeared to be undamaged. The precision of the strike, deep within Iran and with several sensitive sites close by, suggested Israel chose the specific and narrow target, the air defense system.

The radar is the key to any air-defense system. Without radar, the defense system can't track incoming attacks, and its missiles can only fire blindly at fast-moving targets. The rest of the Natanz air-defense systems are useless until the Iranians replace the radar -- and now they know the Israelis can take out it again as fast as they replace it. And they can't see it coming, either. All of their anti-aircraft defense is based on the S-300, which means Israel could nullify it entirely before the Iranians are even aware they're under attack.

This may explain why Iran initially denied any attack. Politically that was the best position for the mullahs in the end anyway, but they sincerely may not have realized what happened. They may also have expected an Israeli response to target their nuclear or oil-production sites with known weaponry that they could detect and attempt to intercept, so when an explosion occurred at a single site, they may well have initially thought it was sabotage. 

They know now, thought, and the mullahs now must consider what this level of precision and accuracy means and rethink all of their defense doctrines. If the Israelis have this facility, then so does the US, and maybe even Jordan, Saudi Arabia, and others. The Iranians don't have the kind of resources to develop effective countermeasures against this new facility of its self-selected enemies. That's because (a) they don't have the resources for it, and (b) they keep pouring resources into proxies like Hamas and Hezbollah to provoke these self-selected enemies. 

This is an existential moment for a very creaky regime that barely can keep the lid on a highly restive population. And the mullahs have to know it. The next strike from Israel won't be limited and it will likely pull down the entire rotted theocracy. 

That's the message Israel sent -- a warning to repent and retreat. Gerald McGlothlin argues at American Thinker that they took a page out of King David's playbook as a warning about what could happen next (via Adam Baldwin):

Targeting Isfahan, Iran's "crown jewel," Israel's action carried a profound warning: a demonstration of military might, and a counterattack that was presumed by many experts not to be made until after Passover.

This maneuver by Israel echoes a biblical story from 1 Samuel 26, where David, pursued by King Saul, infiltrates the king's camp and absconds with his spear and water jug—items placed next to the sleeping king. David's subsequent display of these items from a safe distance served as a powerful testament to his ability to strike at the heart of Saul's defenses without harming him. Similarly, Israel's recent military action against Isfahan sends a clear signal to Iran: "Your military can't protect you from us."

Israel's restraint is both a message and a warning. It signifies that while Israel possesses the capability to unleash devastating strikes that could result in massive casualties and escalate into a larger conflict, it chooses, for now, a path of caution and strategic messaging. This act of restraint should not be mistaken for weakness but rather seen as a calculated effort to avoid unnecessary bloodshed and instability in the region.

Indeed, and one has to wonder just how strong the mullahs' instinct for self-preservation is.