When the Assassins Ezio Auditore da Firenze and Raphael Sánchez traveled to Granada, they found the city to be besieged by Spanish soldiers. They soon discovered it to be a Templar plot, and managed to stop it by freeing King Muhammad XII and persuading him to surrender, in order to swiftly end the conflict.
Ezio then made his way into the city to find any rebelling Templars that remained there. After a short search, he overheard Juan de Marillo and Tomás de Torquemada speaking about their attack on the city, and that anyone who was not in "allegiance of the Pope" to be expelled by force; if they resisted, Tomás would let Juan choose how to punish them.
It also became clear from this conversation that Juan was responsible for the condemning of the Assassins in Barcelona and in Zaragoza. With this in mind, as soon as Torquemada had left, Ezio confronted Juan and assassinated him.