The Iran-Israel Shadow War

From Ally to Existential Enemy

Before 1979, Iran and Israel were close partners. Israel sold weapons to the Shah, trained his intelligence services, and maintained a large diplomatic and business presence in Tehran. The two countries shared a strategic interest in countering Arab nationalism, particularly Nasser's Egypt and Ba'athist Iraq. Israel even helped Iran develop its early nuclear research program.

The Islamic Revolution transformed the relationship overnight. Ayatollah Khomeini declared Israel an illegitimate state that must be eliminated, and support for the Palestinian cause became a core tenet of the Islamic Republic's identity. The Israeli embassy in Tehran was handed to the PLO. 'Death to Israel' became a standard chant at state rallies.

For Israel, Iran's post-revolutionary rhetoric was alarming but not initially an existential concern. The real threat materialized with Iran's nuclear program and its cultivation of Hezbollah as a military force on Israel's northern border. By the 2000s, Israeli leaders had identified Iran as the country's primary strategic threat — a designation that reshaped Israeli defense doctrine, intelligence priorities, and diplomatic strategy.

The Covert Battlefield

The Iran-Israel conflict has been fought largely in the shadows, through operations that both sides often decline to officially acknowledge.

Assassinations of Iranian scientists: Between 2010 and 2020, at least five Iranian nuclear scientists were killed in targeted assassinations widely attributed to Israel's Mossad. The most dramatic was the November 2020 killing of Mohsen Fakhrizadeh, considered the father of Iran's nuclear weapons program, reportedly by a remote-controlled AI-assisted machine gun. Iran accused Israel; Israel neither confirmed nor denied.

Sabotage of nuclear facilities: The Stuxnet computer worm, discovered in 2010, destroyed roughly 1,000 Iranian nuclear centrifuges at the Natanz enrichment facility. It was a joint US-Israeli operation (codenamed Olympic Games) and represented the first known use of a cyberweapon to cause physical destruction of infrastructure. In April 2021, a major explosion at Natanz — attributed to an Israeli sabotage operation using a planted explosive — destroyed the facility's primary power supply.

Iranian retaliation: Iran has attempted operations against Israeli targets abroad, including bombings of Israeli diplomatic missions in the 1990s (Argentina, 1992 and 1994, killing 114 people total) and plots targeting Israeli tourists and diplomats in Thailand, India, Georgia, and other countries. Iran's retaliatory capabilities have generally been less precise and less successful than Israel's operations, though the asymmetry has narrowed.

The Cyber Domain and the Risk of Escalation

The cyber dimension of the Iran-Israel conflict has expanded significantly. After Stuxnet, Iran invested heavily in its own cyber capabilities. Iranian hackers have targeted Israeli water infrastructure, hospitals, and civilian databases. Israel, in turn, allegedly disrupted an Iranian port in 2020 in retaliation for a cyber attack on Israeli water systems.

The shadow war escalated into direct military confrontation in April 2024, when Iran launched over 300 drones and missiles at Israel in response to an Israeli strike on an Iranian diplomatic compound in Damascus that killed senior IRGC commanders. Most projectiles were intercepted by Israeli, American, British, and Jordanian defenses, but the attack crossed a threshold — the first direct Iranian military strike on Israeli territory. Israel responded with a limited strike on Iranian air defense systems near Isfahan.

This exchange demonstrated both the potential for catastrophic escalation and the implicit mutual deterrence that has so far prevented full-scale war. Both sides signaled restraint after striking: Iran declared its attack a proportionate response and considered the matter 'concluded,' while Israel's counterstrike was deliberately limited. The unspoken rules of the shadow war — strike, but don't escalate to the point of open war — held, but barely.