Aguilar played a prominent role in the Brotherhood's actions during the Spanish Inquisition, a period of time in which many members of his Order were captured and executed by the Inquisitors, who acted under the direction of the Templars. He thwarted an attempt by the Grand Inquisitor and Master Templar, Tomás de Torquemada, to obtain an Apple of Eden in order to bring Spain completely under Templar control.
Later, the Spanish Assassins tried to ensure the safety of Prince Ahmed of Granada, the son of Sultan Muhammad XII of Granada, whom the Templars were searching for in order to ransom him against the Apple of Eden they knew to be in the Sultan's possession. Together with Maria, Benedicto, and a number of other Assassins, Aguilar ambushed a Templar force led by Ojeda in a small Andalusian village where the Prince had been hiding.
Despite the Assassins being outnumbered and eventually overpowered, both Aguilar and Maria managed to escape the village with the Prince, though they were quickly pursued by Ojeda and a number of his soldiers. The pursuit lasted some time, but eventually Aguilar was cornered and imprisoned by the Templars.
Following their arrest, the surviving Assassins were transported to Sevilla, where they were denounced as heretics and sentenced to be burned at the stake by Torquemada. In the presence of the king of Aragon and Queen of Castilla Aguilar watched as Ojeda lit the pyre beneath Benedicto’s feet, burning him alive. Despite this, however, Aguilar was able to escape his bonds and engaged the Templars as they closed in. He eventually managed to also free María and together, the two Assassins made their escape through the streets of Sevilla.
Once more pursued by Ojeda and his soldiers, this time across the rooftops of the city, the Assassins made their way to Seville Cathedral, which was under construction at the time. They managed to eliminate several of their Templar pursuers in the process, before finally making their escape by climbing the cathedral’s scaffolding and performing a Leap of Faith into the streets below.
On 2 January 1492, at the urging of the Italian Assassin Ezio Auditore da Firenze - who also happened to be in Spain at the time - Muhammad XII surrendered his capital, Granada, to Torquemada's forces.  As the Templars entered the city both Aguilar and Maria made their way to the Sultan's palace, where they stood watch as the Sultan reluctantly handed over the Apple in exchange for his son's safety, before they made their move.
Dropping smoke bombs into the room, both Assassins quickly eliminated many of the Templars, before Aguilar captured Torquemada and claimed the Apple. Unfortunately for the Assassin however, Ojeda had managed to apprehend Aguilar’s lover, Maria. Ojeda promised to release his captive once Aguilar returned the Apple to Torquemada; Aguilar reluctantly agreed, but before he could act, he witnessed Maria take her own life with Ojeda's blade to prevent him from betraying the Creed to save her life.
Enraged by her death, Aguilar engaged Ojeda in combat but was gradually overcome by his opponent's sheer strength. It was only after he had been knocked to the ground that Aguilar managed to gain the upper hand, using Maria’s launchable Hidden Blade to attack Ojeda and render him defenseless to Aguilar's strikes. With Ojeda dead, a heavily wounded Aguilar was forced to make his escape through the tunnels beneath the palace as Torquemada opened the locked door of the room to the rest of his men.
Aguilar was eventually surrounded on one of the bridges leading from the city, but once more escaped by performing a Leap of Faith into the river far below.
Following the events in Granada, Aguilar realized that the Apple would never be safe from the Templars if it remained in Spain. He made his way to Palos de la Frontera in Huelva, where he charged Christopher Columbus, an ally of the Spanish Assassins, with protecting the Apple.
Following this, Aguilar continued to serve the Assassins; he gained the rank of Master Assassin and eventually became the new Mentor of the Spanish Brotherhood. He died in 1526, having fathered at least one child during his lifetime.
Aguilar's actions ensured the Apple of Eden would remain hidden from both humanity and the Templars, for many centuries, having given it to Columbus, who kept the Apple with him until his death.
In 2016, Abstergo Industries began a search for the Apple, which they believed to have been buried along with Aguilar. To this end, they searched his burial site but were unable to find it. The Templars recovered his equipment in the process and brought it to the Abstergo Foundation facility in Madrid.
In October, Abstergo located the last known descendant of Aguilar, Callum Lynch, and had his execution by lethal injection faked so they could have him relive his ancestor's genetic memories through the Animus 4.3. Callum was outfitted with Aguilar's Hidden Blades (so as to enhance synchronization), and through the Animus session, the location of the Apple was eventually revealed, causing it to fall into the possession of high-ranking Templar Alan Rikkin.
At the end of the Animus session, Aguilar would later appear as a ghostly vision to Callum along with his other Assassin ancestors and mother Mary Lynch, ultimately convincing Callum to embrace his Assassin heritage. Callum would utilize Aguilar's equipment during the Assassins' escape from the facility and assassinate Rikkin in London, reclaiming the Apple.
Aguilar was a committed member of the Assassin Brotherhood, dedicated to preserving free will and fighting against the Knights Templar. He also possessed a deep understanding of the political climate in 15th century Spain and knew Tomás de Torquemada and the Spanish Inquisition had to be stopped.
A capable fighter, Aguilar could handle himself against multiple enemies in both armed and unarmed combat, wielding a range of weapons including swords and spears with great skill. Additionally, he proved to be proficient at archery, using a bow and arrow to deadly effect in both long and close range combat.
Like many Assassins, Aguilar was also trained in freerunning, being able to move across the rooftops of Seville quickly and creatively, ducking in and out of buildings and dashing across ropes in an effort to lose his pursuers. He had also mastered the Leap of Faith, using it on two separate occasions to escape from his enemies.
Equipment-wise, Aguilar possessed dual Hidden Blades as his primary weapons, one of which was equipped with a grappling hook. He also had throwing knives and smoke bombs at his disposal. The robes Aguilar wore showed Moorish influences, being adorned with beads and embroidery.
- Despite the the fact that the Levantine Mentor, Altair Ibn La-Ahad redesigned the Hidden Blade so as to not require the removal of the ring finger, Aguilar still goes through the process of removal and commitment to the Creed.
- Aguilar, and his modern day descendant, Callum Lynch, are both portrayed by Michael Fassbender in the Assassin's Creed.
- "Aguilar" is a Spanish surname meaning "relative to eagles". "De Nerha" is potentially a misspelled form of "De Nerja", which means "From Nerja", with Nerja being an Andalusian town.
- Aguilar was buried with his Hidden Blades, which would later be recovered by Abstergo Industries and used during Callum's Animus sessions to enhance synchronization.
- Aguilar, his descendant Callum, and Maria all wield their primary hidden blade on their right hand wrist in the Assassin's Creed film. Whether this was standard practice of the Spanish Assassins or a select few is unclear.