The film opens with Ezio Auditore da Firenze assassinating the Templar Octavien de Valois to rescue Pantasilea Baglioni. Later, Ezio meets a hooded figure in the streets of Rome to gather intel about his next target, Cesare Borgia, Captain General of the Papal Army and leader of the Italian Templars.
The hooded figure begins to narrate Cesare's rise to power, starting in 1497. After his brother Juan was appointed Captain General, Cesare, then a cardinal, orchestrated his own ascent by manipulating events and using a courtesan to instrumentalize a murder so he could take the place himself. This marked the beginning of Cesare’s ruthless campaign to conquer Romagna, with Ramiro d'Orco, Oliverotto da Fermo and Vitellozzo Vitelli leading his armies. Yet as his grip tightens, dissent grows among his subjects, and cracks begin to appear in his carefully laid plans. The tale reveals how fear and strategic brutality become tools for consolidating power, even as whispers of rebellion ripple through the conquered territories.
Fearing that Cesare no longer needs their services, Oliverotto and Vitellozzo conspire against him. In 1502, they orchestrate a rebellion that seizes significant portions of Cesare's lands. To reclaim control and demonstrate his resolve, Cesare invites the rebel leaders to dinner, offering forgiveness and a chance to return to loyalty. But after the meal, Cesare has his executioner Micheletto Corella kill both Oliverotto and Vitellozzo, a decisive move that cements his reputation as a calculating and merciless leader who will stop at nothing to maintain power.
As the hooded man finishes his story, Ezio vows to kill Cesare and bring an end to his tyranny. After handing Ezio a scroll, the hooded figure heads to Castel Sant'Angelo, where he is revealed to be Leonardo da Vinci. The revelation shifts the chessboard: Cesare greets Leonardo and tells him to return to work building war machines for his army, highlighting the engineer’s crucial role in Cesare’s broader war effort. The moment also deepens Ezio’s resolve, as the assassin recognizes that liberating Rome from Cesare’s grasp will require not only skill and courage but a broader alliance of minds and talents.
Back in the tense atmosphere of Cesare’s world, Leonardo’s presence underscores the blend of politics, warfare, and ingenuity that defines this era. Ezio’s mission is now framed not only as a personal vendetta but as part of a larger, unfolding struggle to free Rome from an increasingly iron‑fisted rule. With the stage set for the events of Brotherhood, the film leaves viewers poised for the next chapter: a city on the brink, where power houses behind grand plans, and where every ally carries the weight of history watching over them.