The twelve-day war between Iran and the Zionist regime in 2025 represented one of the most complex manifestations of hybrid warfare conducted against the Islamic Republic. Within the enemy’s “decapitation strategy,” the primary objective was to collapse Iran’s command structure within the first 48 hours and impose a strategic shock. Yet the political system, centered on the leadership of the Supreme Leader, transformed this threat into a platform for sustainable deterrence. The central question of this study is to explain the role of leadership in reconstructing national command and guiding the country through crisis.

Employing a qualitative explanatory–comparative methodology and a six-level analytical framework (strategic, operational, socio-psychological, spiritual-identity, civilizational, and hybrid), the study argues that the Supreme Leader, by integrating strategic rationality, political spirituality, and media-oriented crisis management, shifted the country from a reactive posture to strategic initiative.

The findings indicate that leadership in the Islamic Republic is not merely a political function; it constitutes the axis of collective will, national meaning-making, and civilizational identity. At the strategic level, the command structure was restored; at the operational level, the government and armed forces were aligned within a unified framework; at the socio-psychological level, the nation became an active participant rather than a passive target; at the spiritual level, faith reinforced the moral legitimacy of decision-making; at the civilizational level, the war was interpreted within the historical confrontation between Islam and global arrogance; and at the hybrid level, military, media, social, and diplomatic dimensions were integrated into a unified command system.

Thus, the twelve-day war offers an indigenous model of multi-level leadership in security crises and provides a conceptual basis for theorizing national security and Islamic civilizational thought.