The precision-guided air operations Israel launched against nuclear facilities, ballistic missile systems, and command-and-control centers in Iran on June 13, 2025, demonstrated that the long-running proxy struggle between the two countries had turned into a direct conventional war.
The killing in these operations of General Mohammad Kazemi, head of the IRGC Intelligence Organization, his deputy Hassan Mohaqqeq, and Brigadier General Gholamreza Mehrabi, deputy intelligence chief of the General Staff, revealed that Israel was pursuing an intelligence-driven “decapitation” strategy. This strategy went beyond merely striking military infrastructure: it sought to systematically dismantle Iran’s strategic decision-making mechanisms and national security architecture.
The attacks’ evolution beyond their kinetic dimension into a multilayered intelligence war once again demonstrated the critical role of superiority in information and analysis in modern conflicts. This article aims to examine, at the interagency level, how Iran’s intelligence apparatus positioned itself in the June 2025 conflict, what operational responses it developed, and what process of restructuring it entered after the conflict.
The Iranian intelligence apparatus’s failure to anticipate either the timing of the attack or its operational focus on senior personnel exposed structural weaknesses in the security bureaucracy. Iran’s organization of its intelligence priorities around internal threats left it unprepared for asymmetric attacks originating abroad. This approach, which did not give sufficient weight to external operational capabilities in its threat assessment matrix, led to a miscalculation of the deterrence threshold. A lack of coordination among intelligence services and interagency rivalry played a critical role in rendering early warning systems ineffective. This strategic blindness laid bare the failure of Iran’s intelligence doctrine, caught between regional power projection and paranoia about internal security.
After the conflict began, Iranian intelligence agencies had to wage a simultaneous struggle on two main fronts: ensuring security and stability at home while directing the capacity for retaliation against Israel abroad. Car bombs detonated in and around Tehran indicated that sabotage cells had been activated. Iran’s Ministry of Intelligence and IRGC intelligence units announced that, through coordinated operations, they had swiftly neutralized Mossad-linked cells allegedly behind these acts. During the same period, the execution on the second day of the war of an already imprisoned individual accused of collaborating with Israel demonstrated that the regime prioritized absolute deterrence against potential domestic threats.
The war, however, continued not only in the physical arena but also in the cyber and psychological spheres. Cyberattacks believed to be backed by Israel briefly interrupted Iranian state television broadcasts and put provocative content on the screen. Iranian intelligence responded with technical measures to regain control of the broadcasts while also restricting internet access nationwide to prevent the spread of disinformation. During the same days, pro-Iranian hacker groups, particularly Handala Hack, retaliated with cyberattacks against Israel. Some Israeli media accounts were taken over, information on Iranian activists opposed to the regime was leaked, and content reinforcing a security-centered public response was circulated.
Another vital intelligence task during the war was to provide Iran’s missile retaliation capability with accurate targets. According to Intelligence Minister Esmail Khatib, sensitive military coordinates were obtained from Israel during the conflict and passed to the Armed Forces. It was claimed that certain targets in Tel Aviv and Haifa were struck on the basis of this information. Iranian intelligence thus sought to demonstrate its ability to support the war effort not only through defensive responses but also through counter-targeting and asymmetric retaliation.
The post-ceasefire response: Consolidating the security state
Although the conflict ended with the ceasefire announced on the morning of June 24, the intelligence war entered a new phase for Iran. The regime further hardened its internal security apparatus to contain the strategic shock created during this period. A total of six people accused of being Mossad agents were executed in the first 72 hours after the ceasefire. These executions aimed to send the public a message of “zero tolerance” not only toward external threats but also toward potential collaborators at home. Hundreds of people were detained nationwide on “suspicion of sabotage,” with large-scale arrest operations conducted particularly in West Azerbaijan, Khuzestan, Kermanshah, and South Khorasan.
The institutional reinforcement of intelligence also accelerated during this period. Major General Majid Khademi was appointed head of the IRGC Intelligence Organization, while commanders killed in the war were given the title “martyrs of conquest.” In statements immediately after the war, Intelligence Minister Esmail Khatib emphasized that they were directly confronting more than 50 foreign intelligence services and claimed that the “documents and digital intelligence” acquired throughout the war had exposed Israel’s vulnerability.
At the same time, Iran’s parliament tightened legislation on espionage offenses. Cooperation with hostile actors was made punishable by death under the charge of “corruption on earth.” By supporting expedited and politically motivated trials, the judiciary expanded the intelligence agencies’ room for maneuver. In this process, Iranian intelligence functioned not only against external threats but also as the principal instrument of consolidation within the regime. Although the ceasefire signaled a military pause, the intelligence war continued to deepen.
Institutional renewal and ideological tightening
After the June war, Iran’s intelligence structure entered a process of restructuring not only in personnel but also in mindset. Major General Majid Khademi, appointed to the IRGC Intelligence Organization, is known as a disciplined and loyal figure. Similarly, Intelligence Minister Esmail Khatib’s repeated emphasis in his statements on “agents of infiltration,” “fronts of sedition,” and “cybernetic infiltrations” indicates that intelligence will focus in the period ahead on internal ideological coherence rather than information originating abroad.
This approach could trap Iranian intelligence in a state of threat-driven vigilance rather than information-based analysis. In particular, Khatib’s statements along the lines of “the enemy is trying to bring down the regime from within; we know this and have done what was necessary” signal a period in which institutional defense rests on loyalty rather than data. Increased coordination among the country’s intelligence institutions, a tougher legal framework, and the normalization of a public “hunt for traitors” show how closely Iranian intelligence has become integrated into the logic of the security state. While this brings intelligence’s role as guardian of the regime to the fore, it also creates a tendency that erodes its capacity for outward-looking strategic foresight.
Conclusion: The intelligence war and the regime’s survival
The June 2025 conflict was a period in which Iranian intelligence had to fight not only the enemy but also its own internal structure. Israel’s precision strikes on highly sensitive targets exposed vulnerabilities in Iran’s security apparatus. While this called intelligence’s preventive capabilities into question, the responses displayed over the following days of the war further increased the regime’s dependence on intelligence. The mass arrests, executions, institutional appointments, and tough legal measures that accompanied the ceasefire demonstrate that intelligence now operates not merely as an information-gathering tool but directly as an apparatus of political repression.
Meanwhile, Iranian intelligence has begun to step up its activities on the territory of other countries in an effort to restore its damaged reputation and regain a measure of psychological advantage. Operatives whom it had placed in these countries, particularly in Europe, over many years, even arranging for them to obtain citizenship, are being exposed for reasons as simple as “writing graffiti on a wall.” More examples of this kind could be cited. Indeed, these countries are openly expressing their discontent with Iran’s activities, and this is leaving Iran increasingly isolated diplomatically as the process unfolds.