Like others of the Inquisition, he believed that rumors of an ongoing Templar conspiracy were little more than "fairy tales". Ironically, the very Templars he did not think existed were manipulating the Inquisition, and it was under their direction that he arrested atheists—actually Assassins—throughout the city. His responsibility for this operation led to his demise at the hands of Italian Assassin Ezio Auditore da Firenze.
In 1491, the Spanish Inquisition had been provided with the names of atheists throughout the country by Rodrigo Borgia, one of the three papal candidates for the upcoming conclave. Unbeknownst to inquisitors such as Pedro, these atheists were actually members of the Assassin Order, and Rodrigo the Grand Master of the Templars.
While inquisitors in Barcelona ousted the local Assassin's guild, arresting Assassins under the orders of the prosecutor Gaspar Martínez, Pedro followed suit in Zaragoza, capturing the first of six Zaragozan Assassins listed by Rodrigo. Despite the brutal torture his tribunal issued to his prisoner, the Assassin resisted all their attempts at conversion or extraction of a confession.
It was during one of these torture sessions that Pedro was paid an unexpected visit by the Grand Inquisitor Tomás de Torquemada. After Torquemada examined the prisoner, amazed at his fearlessness yet disgusted by his defiance to God, he had him executed on the spot for heresy. With that, Pedro departed with Torquemada and their executioner, leaving their dead or dying prisoner to bleed out on the ground. They did not notice when the Italian Assassin Ezio Auditore da Firenze, who had been observing the scene from the windows above, slipped in immediately afterwards to check on his fallen ally.
Shortly afterwards, Pedro met with one of his guard captains at the entrance to his palace, where he received news that four Assassins, all held prisoner in the city catacombs, had escaped. Outraged, the calificador berated his subordinate for incompetence before ordering him to guard the last Assassin at all cost. Accordingly, this last prisoner was moved to a highly-secured location, the top-floor bedroom of the highest tower within the palace.
Almost simultaneously, Ezio sneaked into the palace after Pedro. By the time he rescued the last Assassin, Pedro had left for the city cathedral. Ezio tracked him there, but when finally confronted by his adversary, Pedro recognized him as little more than a mere trespasser. Though the calificador scoffed at Ezio's inquiries about the Templars, believing them to be long extinct, the Assassin killed him anyways.